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Article|01 Sep 2021|OPEN
High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy
Yuhao Gao1, Qinsong Yang1,2, Xinhui Yan1, Xinyue Wu1, Feng Yang1, Jianzhao Li1,3, Jia Wei1, Junbei Ni1, Mudassar Ahmad1, Yuanwen Teng1,4 & Songling Bai 1,
1College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
2Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing 100083, China
3College of Agriculture, Ludong University, Yantai, Shandong 264025, China
4Hainan Institute of Zhejiang University, Sanya, Hainan 572000, China

Horticulture Research 8,
Article number: 197 (2021)
doi: 10.1038/hortres.2021.197
Views: 51

Received: 26 Dec 2020
Revised: 09 Jun 2021
Accepted: 13 Jun 2021
Published online: 01 Sep 2021

Abstract

Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.