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. 2024 Apr 18;19(4):e0299261.
doi: 10.1371/journal.pone.0299261. eCollection 2024.

Transcriptome differential expression analysis of defoliation in different lemon varieties under drought treatment

Meichao Dong  1 , Tuo Yin  2 , Dongguo Zhou  1 , Hanyao Zhang  2 , Fan Yang  1 , Shaohua Wang  1 , Chunrui Long  1 , Xiaomeng Fu  1 , Hongming Liu  1 , Lina Guo  1 , Junyan Gao  1
Affiliations

Transcriptome differential expression analysis of defoliation in different lemon varieties under drought treatment

Meichao Dong et al. PLoS One. .

Abstract

'Allen Eureka' is a bud variety of Eureka lemon with excellent fruiting traits, but severe winter defoliation affects the following year's yield, and the response mechanism of lemon defoliation is currently unknown. Two lemon cultivars ('Allen Eureka' and 'Yunning No. 1') with different defoliation traits were used as materials to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemons. The petiole abscission zone was collected at three different defoliation stages, namely, the predefoliation stage (k15), the middefoliation stage (k30), and the postdefoliation stage (k45). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 1141, 2695, and 1433 differentially expressed genes (DEGs) were obtained in k15, k30, and k45, respectively, and the number of DEGs in k30 was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to hydrolase activity, chitinase activity, oxidoreductase activity, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in k30, which involved plant hormone signal transduction, phenylpropanoid biosynthesis, and biosynthesis of amino acids. The expression trends of some DEGs suggested their roles in regulating defoliation in Lemon. Seven genes were obtained by WGCNA, including sorbitol dehydrogenase (CL9G068822012_alt, CL9G068820012_alt, CL9G068818012_alt), abscisic acid 8'-hydroxylase (CL8G064053012_alt, CL8G064054012_alt), and asparagine synthetase (CL8G065162012_alt, CL8G065151012_alt), suggesting that these genes may be involved in the regulation of lemon leaf abscission.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Changes in enzyme activities during different defoliation periods in two varieties, ’Allen Eureka’ and ’Yunning No. 1’ (Significance is the difference between the two varieties; * p < 0.05, ** p < 0.01, *** p < 0.001).
Fig 2
Fig 2. Changes in endogenous hormone contents during different defoliation periods in two lemon varieties, ’Allen Eureka’ and ’Yunning No. 1’ (Significance is the difference between the two varieties; * p < 0.05, ** p < 0.01, *** p < 0.001).
Fig 3
Fig 3. Principal component analysis (PCA) of differentially expressed genes in ’Allen Eureka’ and ’Yunning No. 1’ lemons at each defoliation period.
Fig 4
Fig 4
(A) Number of DEGs between ’AL’ and ’YN’ for each defoliation period. DEGs were screened according to |log2 (Fold change)| ≥ 1 and padj ≤ 0.05. (B) Venn diagram of ’Allen Eureka’ and ’Yunning No. 1’ for each defoliation period.
Fig 5
Fig 5. GO functional enrichment of differentially expressed genes in ’Allen Eureka’ and ’Yunning No.1’ lemons at each defoliation period.
Fig 6
Fig 6. Enrichment of KEGG metabolic pathways of differentially expressed genes in ’Allen Eureka’ and ’Yunning No.1’ lemons at each defoliation period.
Fig 7
Fig 7. Expression characteristics of differentially expressed genes of the plant hormone signal transduction pathway in ’Allen Eureka’ and ’Yunning No.
1’ lemons at each defoliation period. (The horizontal coordinates of the graphs in the heatmap are the sample names, and the vertical coordinates are the values of the differentially expressed genes after FPKM normalization; the redder the color is, the higher the expression, and the bluer the color is, the lower the expression).
Fig 8
Fig 8. Expression characteristics of differentially expressed genes of metabolic pathways in each defoliation period of the ’Allen Eureka’ and ’Yunning No. 1’ lemons.
(A) Phenylpropanoid biosynthesis; (B) Biosynthesis of amino acids; (C) Amino sugar and nucleotide sugar metabolism; (D) Flavonoid biosynthesis. (The horizontal coordinates of the graph in the heatmap are the sample names, and the vertical coordinates are the values of the differentially expressed genes after normalization of FPKM; the redder the color, the higher the expression, and the bluer the expression, the lower the expression).
Fig 9
Fig 9. Gene clustering tree and module cuts (merging gene modules with similar expression patterns; Different colors represent different modules, the number of genes assigned in a module is clustered according to their expression in a correlation, and genes with higher clusters are assigned to a module).
Fig 10
Fig 10. Different heatmap of module-trait associations.
Fig 11
Fig 11. Gene coexpression network of the turquoise module.
Fig 12
Fig 12. Validation of the expression levels of four differentially expressed genes.
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Grants and funding

This research was funded by National Natural Science Foundation of China (No.31960574); Talent Revitalization Program(2022RC001).