Illumina® Sequencing Reveals Candidate Genes of Carotenoid Metabolism in Three Pummelo Cultivars (Citrus Maxima) with Different Pulp Color

Abstract

Pummelo (Citrus maxima) is one of important fruit trees, which belongs to Citrus species. The fruits of different pummelo cultivars have different colors and differ in the contents of carotenoid. Our results clearly showed that ‘Huangjinmiyou’ (HJMY) has the highest content of β-carotene, followed by ‘Hongroumiyou’ (HRMY) and ‘Guanximiyou’ (GXMY). Lycopene is dominantly accumulated in HRMY. However, the molecular mechanism underlying the carotenoid accumulation in pummelo flesh is not fully understood. In this study, we used the RNA-Seq technique to investigate the candidate genes of carotenoid metabolism in the flesh of pummelo cv. GXMY and its mutants HRMY and HJMY in three development periods of fruit. After data assembly and bioinformatic analysis, a total of 357 genes involved in biosynthesis of secondary metabolites were isolated, of which 12 differentially expressed genes (DEGs) are involved in carotenoid biosynthesis. Among these 12 DEGs, phytoene synthase (PSY2), lycopene β-cyclase (LYCB2), lycopene Ɛ-cyclase (LYCE), carotenoid cleavage dioxygenases (CCD4), 9-cis-epoxycarotenoid dioxygenase (NCED2), aldehyde oxidase 3 (AAO3), and ABA 8′-hydroxylases (CYP707A1) are the most distinct DEGs in three pummelo cultivars. The co-expression analysis revealed that the expression patterns of several transcription factors such as bHLH, MYB, ERF, NAC and WRKY are highly correlated with DEGs, which are involved in carotenoid biosynthesis. In addition, the expression patterns of 22 DEGs were validated by real-time quantitative PCR (RT-qPCR) and the results are highly concordant with the RNA-Seq results. Our results provide a global vision of transcriptomic profile among three pummelo cultivars with different pulp colors. These results would be beneficial to further study the molecular mechanism of carotenoid accumulation in pummelo flesh and help the breeding of citrus with high carotenoid content.

Genomic insights into citrus domestication and its important agronomic traits

“…(2013) 36 CsMADS5 and CsMADS6 Sweet orange – Lu et al. (2018) 37 PSY2 , LYCB2 , LYCE , and CCD4 Pummelo – Jiang et al. (2019) …”

UHPLC-Q-TOF/MS-Based Metabolomics Approach Reveals the Antifungal Potential of Pinocembroside against Citrus Green Mold Phytopathogen

“…Citrus fruit is a major economic crop with a diverse range of species and varieties, including oranges, mandarins, tangerines, pummelos, lemons, citrons, kumquats, limes, and different hybrids [1,2]. Postharvest storage and shelf life of citrus fruit are limited due to the attack of several pathogens such as Penicillium spp., Geotrichum citri-aurantii, Alternaria alternata, and Diaporthe citri being the prevalent postharvest pathogenic fungi in citrus fruit [3][4][5][6].…”

An embedded gene selection method using knockoffs optimizing neural network

“…lycE , which encodes a lycopene beta cyclase, commits the first branch point of lycopene cyclization [ 31 ]. Previous studies have shown that the transcriptional regulation of lycB and lycE are the critical regulatory points in carotenoid biosynthesis [ 32 , 33 ]. VTE4 , which encodes the γ-tocopherol methyltransferase, is a major gene involved in natural phenotypic variation of α-tocopherol.…”