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. 2024 Feb 23:15:1360138.
doi: 10.3389/fgene.2024.1360138. eCollection 2024.

Comparative transcriptome and metabolome profiles of the leaf and fruits of a Xianjinfeng litchi budding mutant and its mother plant

Ning Xu #  1 , Xian-Quan Qin #  1 , Dong-Bo Li  1 , Yan-Jie Hou  1 , Chen Fang  1 , Shu-Wei Zhang  1 , Jing-Yi You  1 , Hong-Li Li  1 , Hong-Ye Qiu  1
Affiliations

Comparative transcriptome and metabolome profiles of the leaf and fruits of a Xianjinfeng litchi budding mutant and its mother plant

Ning Xu et al. Front Genet. .

Abstract

Background: Litchi (Litchi chinensis) is an important sub-tropical fruit in the horticulture market in China. Breeding for improved fruit characteristics is needed for satisfying consumer demands. Budding is a sustainable method for its propagation. During our ongoing breeding program, we observed a litchi mutant with flat leaves and sharp fruit peel cracking in comparison to the curled leaves and blunt fruit peel cracking fruits of the mother plant. Methods: To understand the possible molecular pathways involved, we performed a combined metabolome and transcriptome analysis. Results: We identified 1,060 metabolites in litchi leaves and fruits, of which 106 and 101 were differentially accumulated between the leaves and fruits, respectively. The mutant leaves were richer in carbohydrates, nucleotides, and phenolic acids, while the mother plant was rich in most of the amino acids and derivatives, flavonoids, lipids and organic acids and derivatives, and vitamins. Contrastingly, mutant fruits had higher levels of amino acids and derivatives, carbohydrates and derivatives, and organic acids and derivatives. However, the mother plant's fruits contained higher levels of flavonoids, scopoletin, amines, some amino acids and derivatives, benzamidine, carbohydrates and derivatives, and some organic acids and derivatives. The number of differentially expressed genes was consistent with the metabolome profiles. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enriched gene expressions showed consistent profiles as of metabolome analysis. Conclusion: These results provide the groundwork for breeding litchi for fruit and leaf traits that are useful for its taste and yield.

Keywords: amino acids and derivatives; carbohydrates and derivatives; flavonoid metabolome in fruits; leaf folding; litchi fruit.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phenotypic differences in fruits and leaves of the Xianjinfeng mother plant (N7N) and mutant (N7V).
FIGURE 2
FIGURE 2
Global metabolite profile of leaves and fruits of N7N and N7V litchi. (A) Bar graph showing the number of metabolites detected in each class of compounds. (B) Comparison of the sum of intensities of metabolites in each compound class. (C) Heatmap of relative intensities of metabolites detected in each replicate of the leaf and fruit of N7N and N7V. (D) Principal component analysis, (E) hierarchical clustering, and (F) Pearson’s correlation analysis based on the relative metabolite intensity in N7N and N7V leaves and fruits. The numbers with sample names represent replicates.
FIGURE 3
FIGURE 3
Comparative metabolome profiles of N7NL and N7VL. (A) Volcano plot of DAMs, (B) bar plot of the top 15 DAMs based on VIP scores, (C) scatter plot of KEGG pathways to which DAMs were enriched, and (D) heatmap of log2 fold change values of DAMs in N7NL vs. N7VL, where Alp denotes alcohols and polyols; AlD, alkaloids and derivatives; Am, amines; AAD, amino acids and derivatives; BSD, benzene and substituted derivatives; CAD, carbohydrates and derivatives; Fl, flavonoids; Lip, lipids; NAD, nucleotides and derivatives; OAD, organic acids and derivatives, OHC, organoheterocyclic compounds; OOC, organooxygen compounds; PhA, phenolic acids; Php, phenylpropanoids and polyketides; Phy, phytohormones; and Vit, vitamins.
FIGURE 4
FIGURE 4
Comparative metabolome profiles of N7NF and N7VF. (A) Volcano plot of DAMs, (B) bar plot of the top 15 DAMs based on VIP scores, (C) scatter plot of KEGG pathways to which DAMs were enriched, and (D) heatmap of log2 fold change values of DAMs in N7NF vs. N7VF, where Alp denotes alcohols and polyols; AlD, alkaloids and derivatives; Am, amines; AAD, amino acids and derivatives; BSD, benzene and substituted derivatives; CAD, carbohydrates and derivatives; Fl, flavonoids; Lip, lipids; NAD, nucleotides and derivatives; OAD, organic acids and derivatives, OHC, organoheterocyclic compounds; OOC, organooxygen compounds; PhA, phenolic acids; Php, phenylpropanoids and polyketides; Phy, phytohormones; and Vit, vitamins.
FIGURE 5
FIGURE 5
Transcriptome profile of litchi leaf and fruit. (A) Distribution of FPKM values, (B) principal component analysis, and (C) Pearson’s correlation coefficient of each replicate of leaf and fruit samples of the mother plant (N7N) and mutant (N7V). (D) Quantitative real-time PCR analyses of thirteen litchi genes in leaf and fruit samples of N7N and N7V, where L is leaf and F is fruit. The error bars on the graphs represent ± standard deviation (n = 3).
FIGURE 6
FIGURE 6
Differential gene expression in N7NL and N7VL. (A) Volcano plot of DEGs/DETs, (B) GO enrichment of DEGs/DETs, and (C) KEGG pathway enrichment of DEGs/DETs. (D) Volcano plot of DEGs/DETs, (E) GO enrichment of DEGs/DETs, and (F) KEGG pathway enrichment of DEGs/DETs.
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Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was funded by Guangxi Science and Technology Major Special Project-Breeding and Demonstration Application of New Varieties of Litchi in Guangxi (Grant No. GuiKe AA23023007), China Agriculture Research System of MOF and MARA (Grant No. CARS-32-02), Guangxi Litchi Longan Innovation Team Project of National Modern Agricultural Industrial Technology System (Grant No. nycytxgxcxtd-12-02), and the Lychee and Longan Team Project of Guangxi Academy of Agricultural Sciences (Grant No. GuiNongKe 2021YT043).

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