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

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.

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The genes crucial to carotenoid metabolism under elevated CO2 levels in carrot (Daucus carota L.)

Scientific Reports ◽

10.1038/s41598-021-91522-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongxia Song ◽

Qiang Lu ◽

Leiping Hou ◽

Meilan Li

Keyword(s):

Molecular Mechanism ◽

Daucus Carota ◽

Carotenoid Biosynthesis ◽

Practical Significance ◽

Carotenoid Content ◽

Rna Seq ◽

Daucus Carota L ◽

Carotenoid Metabolism ◽

Biological Yield ◽

Missed Opportunity

AbstractThe CO2 saturation point can reach as high as 1819 μmol· mol−1 in carrot (Daucus carota L.). In recent years, carrot has been cultivated in out-of-season greenhouses, but the molecular mechanism of CO2 enrichment has been ignored, and this is a missed opportunity to gain a comprehensive understanding of this important process. In this study, it was found that CO2 enrichment increased the aboveground and belowground biomasses and greatly increased the carotenoid contents. Twenty genes related to carotenoids were discovered in 482 differentially expressed genes (DEGs) through RNA sequencing (RNA-Seq.). These genes were involved in either carotenoid biosynthesis or the composition of the photosystem membrane proteins, most of which were upregulated. We suspected that these genes were directly related to quality improvement and increases in biomass under CO2 enrichment in carrot. As such, β-carotene hydroxylase activity in carotenoid metabolism and the expression levels of coded genes were determined and analysed, and the results were consistent with the observed change in carotenoid content. These results illustrate the molecular mechanism by which the increase in carotenoid content after CO2 enrichment leads to the improvement of quality and biological yield. Our findings have important theoretical and practical significance.

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Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

International Journal of Molecular Sciences ◽

10.3390/ijms19124006 ◽

2018 ◽

Vol 19 (12) ◽

pp. 4006 ◽

Cited By ~ 1

Author(s):

Xi Li ◽

Dongqin Tang ◽

Hui Du ◽

Yimin Shi

Keyword(s):

Flower Color ◽

Carotenoid Biosynthesis ◽

Carotenoid Content ◽

Rna Seq ◽

Color Formation ◽

Light Yellow ◽

Color Fading ◽

Narcissus Pseudonarcissus ◽

Bulbous Plant ◽

Β Carotene

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

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Strigolactone Signaling Genes Showing Differential Expression Patterns in Arabidopsis max Mutants

Plants ◽

10.3390/plants8090352 ◽

2019 ◽

Vol 8 (9) ◽

pp. 352 ◽

Cited By ~ 4

Author(s):

Manu Kumar ◽

Inyoung Kim ◽

Yeon-Ki Kim ◽

Jae Bok Heo ◽

Mi Chung Suh ◽

...

Keyword(s):

Signal Transduction ◽

Protein Kinase ◽

Differential Expression ◽

Candidate Genes ◽

Molecular Mechanism ◽

Regulatory Mechanism ◽

Expression Patterns ◽

Shoot Branching ◽

Biosynthesis Pathway

Strigolactone (SL) is a recently discovered class of phytohormone that inhibits shoot branching. The molecular mechanism underlying SL biosynthesis, perception, and signal transduction is vital to the plant branching phenotype. Some aspects of their biosynthesis, perception, and signaling include the role of four MORE AXILLARY GROWTH genes, MAX3, MAX4, MAX1, and MAX2. It is important to identify downstream genes that are involved in SL signaling. To achieve this, we studied the genomic aspects of the strigolactone biosynthesis pathway using microarray analysis of four max mutants. We identified SL signaling candidate genes that showed differential expression patterns in max mutants. More specifically, 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 4 (ACC4) and PROTEIN KINASE 3 (PKS3) displayed contrasting expression patterns, indicating a regulatory mechanism in SL signaling pathway to control different phenotypes apart from branching phenotype.

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RNA-Seq reveals differential expression patterns of genes associated with carotenoid accumulation in loquat

Acta Physiologiae Plantarum ◽

10.1007/s11738-017-2463-0 ◽

2017 ◽

Vol 39 (8) ◽

Cited By ~ 1

Author(s):

Ting-ting Zheng ◽

Zhi-ke Zhang ◽

Muhammad Qasim Shahid ◽

Wei-ling Wei ◽

Faheem Shehzad Baloch ◽

...

Keyword(s):

Differential Expression ◽

Expression Patterns ◽

Rna Seq ◽

Carotenoid Accumulation

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Changes in Fruit pigment accumulation, chloroplast development, and Transcriptome analysis in the CRISPR/Cas9-Mediated Knockout of Stay-green 1 (slsgr1) Mutant

Food Quality and Safety ◽

10.1093/fqsafe/fyab029 ◽

2021 ◽

Author(s):

Liqun Ma ◽

Ni Zeng ◽

Ke Cheng ◽

Jinyan Li ◽

Keru Wang ◽

...

Keyword(s):

Color Change ◽

Tomato Fruit ◽

Carotenoid Biosynthesis ◽

Carotenoid Content ◽

Rna Seq ◽

Loss Of Function ◽

Stay Green ◽

Pigment Accumulation ◽

Brown Color

Abstract The tomato fruit of green-flesh (gf) mutant ripen to a muddy brown color and has been demonstrated previously to be a loss-of-function mutant. Here, we provide more evidence to support this view that SlSGR1 involved in color change in ripening tomato fruits. Knocking out SlSGR1 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy showed obviously a muddy brown color with significantly higher chlorophyll and carotenoid content compared with WT fruits. To further verify the role of SlSGR1 in fruit color change, we performed RNA-seq analysis, where a total of 354 differentially expressed genes (124/230 down-/upregulated) were identified between WT and slsgr1. Additionally, the expression of numerous genes associated with photosynthesis and chloroplast function changed significantly when SlSGR1 was knocked out. Taken together, these results indicate that SlSGR1 is involved color change in ripening fruit via chlorophyll degradation and carotenoid biosynthesis.

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Effects of Exogenous Abscisic Acid (ABA) on Carotenoids and Petal Color in Osmanthus fragrans ‘Yanhonggui’

Plants ◽

10.3390/plants9040454 ◽

2020 ◽

Vol 9 (4) ◽

pp. 454

Author(s):

Yucheng Liu ◽

Bin Dong ◽

Chao Zhang ◽

Liyuan Yang ◽

Yiguang Wang ◽

...

Keyword(s):

Abscisic Acid ◽

Metabolic Pathway ◽

Carotenoid Biosynthesis ◽

Carotenoid Content ◽

Native Plant ◽

Total Carotenoids ◽

Osmanthus Fragrans ◽

Carotenoid Accumulation ◽

Β Carotene ◽

Carotenoid Degradation

Osmanthus fragrans is a well-known native plant in China, and carotenoids are the main group of pigments in the petals. Abscisic acid (ABA) is one of the products of the metabolic pathway of carotenoids. Application of ABA could affect pigmentation of flower petals by changing the carotenoid content. However, little is known about the effects of ABA treatment on carotenoid accumulation in O. fragrans. In this study, different concentrations of ABA (0, 150 and 200 mg/L) were spread on the petals of O. fragrans ‘Yanhonggui’. The petal color of ‘Yanhonggui’ receiving every ABA treatment was deeper than that of the control. The content of total carotenoids in the petals significantly increased with 200 mg/L ABA treatment. In the petals, α-carotene and β-carotene were the predominant carotenoids. The expression of several genes involved in the metabolism of carotenoids increased with 200 mg/L ABA treatment, including PSY1, PDS1, Z-ISO1, ZDS1, CRTISO, NCED3 and CCD4. However, the transcription levels of the latter two carotenoid degradation-related genes were much lower than of the five former carotenoid biosynthesis-related genes; the finding would explain the significant increase in total carotenoids in ‘Yanhonggui’ petals receiving the 200 mg/L ABA treatment.

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Repression of Carotenoid Accumulation by Nitrogen and NH4+ Supply in Carrot Callus Cells In Vitro

Plants ◽

10.3390/plants10091813 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1813

Author(s):

Tomasz Oleszkiewicz ◽

Michał Kruczek ◽

Rafal Baranski

Keyword(s):

Callus Growth ◽

Carotenoid Content ◽

N Availability ◽

Carotenoid Accumulation ◽

Carotenoid Metabolism ◽

Ammonium N ◽

Dark Orange ◽

Modified Media ◽

Orange Color

The effect of mineral nutrition on the accumulation of the main health beneficial compounds in carrots, the carotenoid pigments, remains ambiguous; here, a model-based approach was applied to reveal which compounds are responsible for the variation in carotenoid content in carrot cells in vitro. For this purpose, carotenoid-rich callus was cultured on either BI (modified Gamborg B5) or R (modified Murashige and Skoog MS) mineral media or on modified media obtained by exchanging compounds between BI and R. Callus growing on the BI medium had abundant carotene crystals in the cells and a dark orange color in contrast to pale orange callus with sparse crystals on the R medium. The carotenoid content, determined by HPLC and spectrophotometrically after two months of culture, was 5.3 higher on the BI medium. The replacement of media components revealed that only the N concentration and the NO3:NH4 ratio affected carotenoid accumulation. Either the increase of N amount above 27 mM or decrease of NO3:NH4 ratio below 12 resulted in the repression of carotenoid accumulation. An adverse effect of the increased NH4+ level on callus growth was additionally found. Somatic embryos were formed regardless of the level of N supplied. Changes to other media components, i.e., macroelements other than N, microelements, vitamins, growth regulators, and sucrose had no effect on callus growth and carotenoid accumulation. The results obtained from this model system expand the range of factors, such as N availability, composition of N salts, and ratio of nitrate to ammonium N form, that may affect the regulation of carotenoid metabolism.

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Carotenoid Production by Dunaliella salina under Red Light

Antioxidants ◽

10.3390/antiox8050123 ◽

2019 ◽

Vol 8 (5) ◽

pp. 123 ◽

Cited By ~ 10

Author(s):

Yanan Xu ◽

Patricia J. Harvey

Keyword(s):

Blue Light ◽

White Light ◽

High Intensity ◽

Dunaliella Salina ◽

Red Light ◽

Carotenoid Biosynthesis ◽

High Rate ◽

Carotenoid Content ◽

Photon Flux ◽

Carotenoid Accumulation

The halotolerant photoautotrophic marine microalga Dunaliella salina is one of the richest sources of natural carotenoids. Here we investigated the effects of high intensity blue, red and white light from light emitting diodes (LED) on the production of carotenoids by strains of D. salina under nutrient sufficiency and strict temperature control favouring growth. Growth in high intensity red light was associated with carotenoid accumulation and a high rate of oxygen uptake. On transfer to blue light, a massive drop in carotenoid content was recorded along with very high rates of photo-oxidation. In high intensity blue light, growth was maintained at the same rate as in red or white light, but without carotenoid accumulation; transfer to red light stimulated a small increase in carotenoid content. The data support chlorophyll absorption of red light photons to reduce plastoquinone in photosystem II, coupled to phytoene desaturation by plastoquinol:oxygen oxidoreductase, with oxygen as electron acceptor. Partitioning of electrons between photosynthesis and carotenoid biosynthesis would depend on both red photon flux intensity and phytoene synthase upregulation by the red light photoreceptor, phytochrome. Red light control of carotenoid biosynthesis and accumulation reduces the rate of formation of reactive oxygen species (ROS) as well as increases the pool size of anti-oxidant.

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Transcriptome Profiling Analysis of Muscle Tissue Reveals Potential Candidate Genes Affecting Water Holding Capacity in Chinese Simmental Beef Cattle

10.21203/rs.3.rs-153911/v1 ◽

2021 ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Rna Seq ◽

Protein Protein Interaction ◽

Water Holding

Abstract Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were subjected to RNA sequencing (RNA-seq), among which eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 1256 genes were identified as differentially expressed genes (DEGs) between two groups, of which 948 genes were up-regulated and 308 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 24 GO terms and 78 pathways. Additionally, based on protein-protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARg, MYH10, MYL2, MYPN, and TPI1) influenced WHC in accordance with previous studies, but also identified six genes (ITGAV, FGF2, THBS1, DCN, COL4A1, and TGFBR1) as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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Evaluation of Carotenoids Accumulation and Biosynthesis in Two Genotypes of Pomelo (Citrus maxima) during Early Fruit Development

Molecules ◽

10.3390/molecules26165054 ◽

2021 ◽

Vol 26 (16) ◽

pp. 5054

Author(s):

Yihan Zhao ◽

Xufeng Yang ◽

Yuwei Hu ◽

Qiuming Gu ◽

Weiling Chen ◽

...

Keyword(s):

Fruit Development ◽

Early Stage ◽

Expression Patterns ◽

Carotenoid Content ◽

Carotenogenic Genes ◽

Citrus Maxima ◽

Regulation Mechanisms ◽

Rate Limiting ◽

Insight Into ◽

Β Carotene

Pomelo is rich in bioactive compounds (carotenoids, phenolics and essential oil) in the early stage of fruit development, but it is often wasted in the cultivation and management process. To gain an insight into the carotenoid metabolism pathway in pomelo, the carotenoid profiles and the expression patterns of carotenogenic genes were investigated in two genotypes of pomelo during early fruit development. The results showed that a higher carotenoid content was observed in honey pomelo as compared with golden pomelo, which may be related to different gene regulation mechanisms. Lutein, a-carotene, and β-carotene were the main carotenoids in pomelo young fruit, and lutein was the highest one. The accumulation of carotenoids during fruit early development in honey pomelo is related to the transcriptional regulation of ZISO and LUT5. In golden pomelo, the rate-limiting gene for carotenoids is PDS and ZDS. In addition, the expression of seven genes except CRTISO in honey pomelo was higher than that in golden pomelo. The results are helpful to further clarify the regulatory mechanism of carotenoid accumulation during early fruit development and provide a direction for the high-value utilization of young fruits in pomelo.

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