Transcriptome differential expression analysis of defoliation of two different lemon varieties

Meichao Dong; Tuo Yin; Junyan Gao; Hanyao Zhang; Fan Yang; Shaohua Wang; Chunrui Long; Xiaomeng Fu; Hongming Liu; Lina Guo; Dongguo Zhou

doi:10.7717/peerj.17218

Transcriptome differential expression analysis of defoliation of two different lemon varieties

PeerJ. 2024 Apr 26:12:e17218. doi: 10.7717/peerj.17218. eCollection 2024.

Authors

Affiliations

¹ Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China.
² The Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, College of Forestry, Southwest Forestry University, Kunming, China.

Abstract

'Allen Eureka' is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree's growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars ('Allen Eureka' and 'Yunning No. 1') with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and analysis of defoliation pathways.

Keywords: Defoliation; Differentially expressed genes; Lemon; Transcriptome; WGCNA.

Publication types

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

MeSH terms

Citrus* / genetics
Citrus* / growth & development
Citrus* / metabolism
Gene Expression Profiling*
Gene Expression Regulation, Plant*
Plant Leaves* / genetics
Plant Leaves* / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism
Transcriptome*

Substances

Transcription Factors

Grants and funding

This research was funded by National Natural Science Foundation of China (No. 31960574); Talent Revitalization Program(2022RC001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.