Preliminary Transcriptome Analysis in Two Tomato Fruits Materials with Different Sugar Content

doi:10.16420/j.issn.0513-353x.2023-0761

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (2): 281-294.doi: 10.16420/j.issn.0513-353x.2023-0761

• Genetic&Breeding?Germplasm Resources?Molecular Biology • Previous Articles Next Articles

Preliminary Transcriptome Analysis in Two Tomato Fruits Materials with Different Sugar Content

ZHANG Wenhao¹^,², ZHANG Hui¹, LIU Yuting¹, WANG Yan³, ZHANG Yingying¹, WANG Xinman¹, WANG Quanhua², ZHU Weimin¹, YANG Xuedong¹^,^*()

¹ Shanghai Key Laboratory of Protected Horticulture Technology，Horticulture Research lnstitute，Shanghai Academy of Agricultural Sciences，Shanghai 201413，China
² College of Life Sciences，Shanghai Normal University，Shanghai 201400，China
³ Horticulture Research lnstitute，Anhui Academy of Agricultural Sciences，Hefei 230031，China

Received:2023-12-18 Revised:2024-01-14 Online:2024-02-25 Published:2024-02-26
Contact: YANG Xuedong

Abstract

Abstract:

High sugar（8%）and common sugar（4.5%）tomatoes were used as the research materials. Fruit samples were collected at the mature green stage，the breaker stage，the pink stage，and the red ripe stage. Transcriptome sequencing was conducted to analyze the differences in gene expression between these two materials. The analysis revealed there 288 differentially expressed genes（DEGs）between common and high sugar tomatoes across these four stages，with 174 down-regulated DEGs and 114 up-regulated DEGs. Notably，the breaker stage showed the highest number of DEGs between these two materials. GO analysis demonstrated significant enrichment of DEGs and GO terms at the breaker stage with the greatest number of GO terms identified at this stage. Furthermore，KEGG analysis showed that the DEGs and related pathways，particularly sugar and acid metabolism pathways，were concentrated at the breaker stage. Clustering analysis of key enzyme genes involved in sugar and acid metabolism identified 30 DEGs.

Key words: tomato, sugar content, maturity stage, transcriptome analysis

ZHANG Wenhao, ZHANG Hui, LIU Yuting, WANG Yan, ZHANG Yingying, WANG Xinman, WANG Quanhua, ZHU Weimin, YANG Xuedong. Preliminary Transcriptome Analysis in Two Tomato Fruits Materials with Different Sugar Content[J]. Acta Horticulturae Sinica, 2024, 51(2): 281-294.

Figures/Tables 11

Fig. 1 The changes in main sugars and acids between common and high sugar tomatoes Different lowercase letters in the same material indicate significant differences among different stage at 0.05 level.

Fig. 2 The box diagram of gene expression distribution between common and high sugar tomatoes

Fig. 3 Number of DEGs between common and high sugar tomatoes

Table 1 The enrichment quantity of DEGs in GO between common and high sugar tomatoes

时期 Developmental stage	GO数量 All GOs	总差异基因 All DEGs	下调差异基因 Down-regulated DEGs	上调差异基因 Up-regulated DEGs
绿熟期Mature green	673	5 163	2 524	2 639
转色期Breaker	768	8 544	3 351	5 193
粉红期Pink	651	3 293	1 832	1 461
红熟期Red ripe	657	4 552	2 495	2 057

Fig. 4 The top 30 GO terms with significant difference between common and high sugar tomatoes

Table 2 The enrichment analysis of DEGs in pathways between common and high sugar tomatoes

发育时期 Developmental stage	通路数量 Pathways	总差异基因 All DEGs	下调差异基因 Down-regulated DEGs	上调差异基因 Up-regulated DEGs
绿熟期Mature green	105	802	443	359
转色期Breaker	116	1 406	668	738
粉红期Pink	100	521	252	269
红熟期Red ripe	106	725	392	333

Fig. 5 The comparison of key KEGG pathways between common and high sugar tomatoes

Fig. 6 The pathways of sugar and acid metabolism enriched by KEGG between high sugar and common tomatoes

Fig. 7 The heat map of DEGs in sugar and acid metabolism pathways between high sugar and common tomatoes enriched by KEGG A：Sucrose synthase SS，sucrose phosphate synthase SPS；B：Hexokinase HXK，fructose kinase FK；C：Acid and neutral invertase；D：Phosphoenolpyruvate carboxylase PEPC，malate dehydrogenase MDH，citrate synthase CS；E：Starch synthase，α-amylase，β-amylase；F：Trehalose synthase TPS，trehalose acidification enzyme TPP. H：High sugar tomato；L：Common tomato；G：Mature green stage；B：Breaker stage；P：Pink stage；R：Red ripe stage.

Fig. 8 The clustering analysis of DEGs in sugar and acid metabolism pathways between high sugar and common tomatoes H：High sugar tomato；L：Common tomato；G：Mature green stage；B：Breaker stage；P：Pink stage；R：Red ripe stage.

Fig. 9 Validation of DEGs transcriptome sequencing（FPKM）and qRT-PCR relative expression（relative）assays between high sugar and common tomatoes

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Preliminary Transcriptome Analysis in Two Tomato Fruits Materials with Different Sugar Content

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