Integrated Metabolome and Transcriptome Analysis Unveils Novel Pathway Involved in the Formation of Yellow Peel in Cucumber.

Juan Chen,Huiming Chen,Chen Chen,Xiaohong Liu,Geng Zhou,Yun Tian,Xiangyang Lu

doi:10.3390/ijms22031494

Abstract

Yellow peel will adversely affect the appearance quality of cucumber fruit, but the metabolites and the molecular mechanism of pigment accumulation in cucumber peel remain unclear. Flavonoid metabolome and transcriptome analyses were carried out on the young peel and old peel of the color mutant L19 and the near-isogenic line L14. The results showed that there were 165 differential flavonoid metabolites in the old peel between L14 and L19. The total content of representative flavonoid metabolites in the old peel of L14 was 95 times that of L19, and 35 times that of young peel of L14, respectively. This might explain the difference of pigment accumulation in yellow peel. Furthermore, transcriptome analysis showed that there were 3396 and 1115 differentially expressed genes in the yellow color difference group (Young L14 vs. Old L14 and Old L14 vs. Old L19), respectively. These differentially expressed genes were significantly enriched in the MAPK signaling pathway–plant, plant–pathogen interaction, flavonoid biosynthesis and cutin, suberine and wax biosynthesis pathways. By analyzing the correlation between differential metabolites and differentially expressed genes, six candidate genes related to the synthesis of glycitein, kaempferol and homoeriodictyol are potentially important. In addition, four key transcription factors that belong to R2R3-MYB, bHLH51 and WRKY23 might be the major drivers of transcriptional changes in the peel between L14 and L19. Then, the expression patterns of these important genes were confirmed by qRT-PCR. These results suggested that the biosynthesis pathway of homoeriodictyol was a novel way to affect the yellowing of cucumber peel. Together, the results of this study provide a research basis for the biosynthesis and regulation of flavonoids in cucumber peel and form a significant step towards identifying the molecular mechanism of cucumber peel yellowing.

Highlights

Cucumber (Cucumis sativus L.), which belongs to the annual herb of muskmelon of Cucurbitaceae, is an economically important crop worldwide [1]
The results showed that DEGs in YL14_vs_OL14, YL14_vs_YL19 and OL14_vs_OL19 were enriched in the metabolic pathways, biosynthesis of secondary metabolites pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway and photosynthesis-antenna proteins pathway
Because the yellow peel of cucumber and its corresponding mutants are difficult to obtain, or the collected materials are greatly affected by the environment, and their stability cannot be guaranteed, the research progress of peel yellow gene is slow

Summary

Introduction

Cucumber (Cucumis sativus L.), which belongs to the annual herb of muskmelon of Cucurbitaceae, is an economically important crop worldwide [1]. Cucumber is native to India, but widely planted in temperate and tropical regions all over the world [2,3,4,5]. Peel color is an important standard of food cucumber quality traits, which can greatly affect consumers’ choices, so it has an important commodity value [8]. The commodity value of cucumber peel color has strong regional characteristics, so consumers in different regions have different preferences for it, and it is impossible to use a unified standard to judge the quality of a certain peel color. Combining with the market demands of cucumber, it is an important breeding goal to improve the economic value through perfecting peel color

Methods

Results

Conclusion