SRNAome and transcriptome analysis provide insight into strawberry fruit ripening

Yunxiang Wang; Wensheng Li; Hong Chang; Jiahua Zhou; Yunbo Luo; Kaichun Zhang; Jinhua Zuo; Baogang Wang

doi:10.1016/j.ygeno.2020.01.008

SRNAome and transcriptome analysis provide insight into strawberry fruit ripening

Genomics. 2020 May;112(3):2369-2378. doi: 10.1016/j.ygeno.2020.01.008. Epub 2020 Jan 13.

Authors

Yunxiang Wang¹, Wensheng Li¹, Hong Chang¹, Jiahua Zhou¹, Yunbo Luo², Kaichun Zhang¹, Jinhua Zuo³, Baogang Wang⁴

Affiliations

¹ Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China.
² College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
³ Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China. Electronic address: zuojinhua@nercv.org.
⁴ Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China; National R&D Center For Fruit Processing, Beijing 100093, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China. Electronic address: wangbaogang@baafs.net.cn.

PMID: 31945464
DOI: 10.1016/j.ygeno.2020.01.008

Abstract

Strawberry fruit ripening is a complex process affected by multiple factors at different regulation levels. To elucidate the regulation mechanisms, the combined analysis of sRNAome and transcriptome were used. A total of 124 known and 190 novel miRNAs were found, 62 of them were significantly differentially expressed (DE). The targets of the DE miRNAs were parsed and several TFs, such as SPL, ARF, WRKY, and TCP, were found to be involved in ripening. Elevated CO₂ can significantly postpone ripening and miR156, miR166f, miR171a, and miR171d were the DE miRNAs. Transcriptome analysis found 313 DE genes related to fruit ripening, including cell wall metabolism-related genes, color-related genes, ethylene-related genes, and genes encoding TFs such as MYB, SPL, NAC, TCP, and ARF. Based on above, a combined regulatory model involved in fruit ripening was created. These results provide valuable information for understanding the complicated coordinated regulatory network of strawberry fruit ripening.

Keywords: Degradome analysis; Strawberry fruit ripening; Transcriptome; miRNAs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Carbon Dioxide
Fragaria / genetics*
Fragaria / growth & development
Fragaria / metabolism
Fruit / genetics*
Fruit / growth & development
Fruit / metabolism
Gene Expression Profiling
Gene Expression Regulation, Plant*
Gene Regulatory Networks
MicroRNAs / metabolism*
RNA, Messenger / metabolism

Substances

MicroRNAs
RNA, Messenger
Carbon Dioxide