Comprehensive metabolome and transcriptome analyses shed light on the regulation of SlNF-YA3b in carotenoid biosynthesis in tomato fruit.

Fruit are an important source of human dietary nutrition, in which carotenoids are crucial for their appearance and nutritional quality. However, the regulatory network of carotenoid biosynthesis in the fruit of horticultural crops remains obscure. Here, a natural tomato mutant, yellowing mutant (ym), in the genetic background of Solanum lycopersicum cultivar 'Zhongshu 4' (ZS4) was investigated. Phenotypic analysis showed that the coloring of ym fruit was delayed compared to their wild type, and carotenoid content in ym fruit was significantly lower than that of ZS4 fruit. Integrative metabolome and transcriptome profiling was used to analyze the dynamic changes of carotenoid metabolite content and gene expression in ZS4 and ym fruit during ripening, and differences in carotenoid metabolite content and gene expression between ZS4 and ym fruit were compared. In contrast to ZS4 fruit, the content of carotenes dramatically decreased in ym fruit, of which phytoene and lycopene levels were down-regulated in ym throughout fruit ripening. In the process of fruit ripening, the transcriptome fluctuation of ym was obviously stronger than that of ZS4. Differences in gene expression between ZS4 and ym gradually reduced with fruit ripening. Furthermore, 105 consistently up-regulated and 113 consistently down-regulated genes were found in ym fruit during ripening. KEGG pathway enrichment analyses indicated that differentially expressed genes between ZS4 and ym were implicated in the carotenoid biosynthesis pathway. Correlation analysis showed that 28 genes were positively correlated with phytoene and lycopene content, including SlNF-YA3b (Solyc12G000315) encoding an NF-YA subunit of nuclear factor Y (NF-Y) transcription factors. Expression analysis exhibited that SlNF-YA3b presented a ripening-related expression pattern. Virus-induced gene silencing demonstrated that SlNF-YA3b positively regulated carotenoid accumulation in tomato fruit. Yeast-one hybrid and transcriptional activity assays showed that SlNF-YA3b could bind to the promoter of the carotenogenic gene SlPDS (Solyc03G003570) and promote its transcription. These data suggest that SlNF-YA3b may participate in the regulation of carotenoid biosynthesis in tomato fruit by directly activating the expression of SlPDS. Our findings not only achieve deeper insights into the regulatory mechanisms of carotenoid biosynthesis in the fruit of horticultural crops but also provide better guidance for the improvement of fruit quality maintenance technologies. • Integrated metabolome and transcriptome analyses are performed in ym fruit. • Phytoene and lycopene are critical for the abnormal coloration of ym fruit. • A total of 28 genes are correlated with phytoene and lycopene in tomato fruit. • SlNF-YA3b positively regulates carotenoid accumulation in tomato fruit. • SlNF-YA3b activates the expression of SlPDS by binding its promoter. [ABSTRACT FROM AUTHOR]