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The first domesticated carrots were thought to be purple carrots rich in anthocyanins. The anthocyanins biosynthesis in solid purple carrot taproot was regulated by DcMYB7 within P3 region containing a gene cluster of six DcMYBs. Here, we described a MYB gene within the same region, DcMYB11c, which was highly expressed in the purple pigmented petioles. Overexpression of DcMYB11c in 'Kurodagosun' (KRDG, orange taproot carrot with green petioles) and 'Qitouhuang' (QTHG, yellow taproot carrot with green petioles) resulted in deep purple phenotype in the whole carrot plants indicating anthocyanins accumulation. Knockout of DcMYB11c in 'Deep Purple' (DPPP, purple taproot carrot with purple petioles) through CRISPR/Cas9‐based genome editing resulted in pale purple phenotype due to the dramatic decrease of anthocyanins content. DcMYB11c could induce the expression of DcbHLH3 and anthocyanins biosynthesis genes to jointly promote anthocyanins biosynthesis. Yeast one‐hybrid assay (Y1H) and dual‐luciferase reporter assay (LUC) revealed that DcMYB11c bound to the promoters of DcUCGXT1 and DcSAT1 and directly activated the expression of DcUCGXT1 and DcSAT1 responsible for anthocyanins glycosylation and acylation, respectively. Three transposons were present in the carrot cultivars with purple petioles but not in the carrot cultivars with green petioles. We revealed the core factor, DcMYB11c, involved in anthocyanins pigmentation in carrot purple petioles. This study provides new insights into precise regulation mechanism underlying anthocyanins biosynthesis in carrot. The orchestrated regulation mechanism in carrot might be conserved across the plant kingdom and useful for other researchers working on anthocyanins accumulation in different tissues. Summary statement: Here, we described a MYB gene, DcMYB11c, which was highly expressed in the purple pigmented petioles. The orchestrated regulation mechanism in carrot might be conserved across the plant kingdom and useful for other researchers working on anthocyanins accumulation in different tissues. [ABSTRACT FROM AUTHOR]

Background: Betalain is a natural pigment with important nutritional value and broad application prospects. Previously, we produced betanin biosynthesis transgenic carrots via expressing optimized genes CYP76AD1S, cDOPA5GTS and DODA1S. Betanin can accumulate throughout the whole transgenic carrots. But the effects of betanin accumulation on the metabolism of transgenic plants and whether it produces unexpected effects are still unclear. Results: The accumulation of betanin in leaves can significantly improve its antioxidant capacity and induce a decrease of chlorophyll content. Transcriptome and metabolomics analysis showed that 14.0% of genes and 33.1% of metabolites were significantly different, and metabolic pathways related to photosynthesis and tyrosine metabolism were markedly altered. Combined analysis showed that phenylpropane biosynthesis pathway significantly enriched the differentially expressed genes and significantly altered metabolites. Conclusions: Results showed that the metabolic status was significantly altered between transgenic and non-transgenic carrots, especially the photosynthesis and tyrosine metabolism. The extra consumption of tyrosine and accumulation of betanin might be the leading causes. [ABSTRACT FROM AUTHOR]

SUMMARY: The accumulation of carotenoids, such as xanthophylls, lycopene, and carotenes, is responsible for the color of carrot (Daucus carota subsp. sativus) fleshy roots. The potential role of DcLCYE, encoding a lycopene ε‐cyclase associated with carrot root color, was investigated using cultivars with orange and red roots. The expression of DcLCYE in red carrot varieties was significantly lower than that in orange carrots at the mature stage. Furthermore, red carrots accumulated larger amounts of lycopene and lower levels of α‐carotene. Sequence comparison and prokaryotic expression analysis revealed that amino acid differences in red carrots did not affect the cyclization function of DcLCYE. Analysis of the catalytic activity of DcLCYE revealed that it mainly formed ε‐carotene, while a side activity on α‐carotene and γ‐carotene was also observed. Comparative analysis of the promoter region sequences indicated that differences in the promoter region may affect the transcription of DcLCYE. DcLCYE was overexpressed in the red carrot 'Benhongjinshi' under the control of the CaMV35S promoter. Lycopene in transgenic carrot roots was cyclized, resulting in the accumulation of higher levels of α‐carotene and xanthophylls, while the β‐carotene content was significantly decreased. The expression levels of other genes in the carotenoid pathway were simultaneously upregulated. Knockout of DcLCYE in the orange carrot 'Kurodagosun' by CRISPR/Cas9 technology resulted in a decrease in the α‐carotene and xanthophyll contents. The relative expression levels of DcPSY1, DcPSY2, and DcCHXE were sharply increased in DcLCYE knockout mutants. The results of this study provide insights into the function of DcLCYE in carrots, which could serve as a basis for creating colorful carrot germplasms. Significance Statement: In this study, we found that the accumulation of lycopene and carotenes in carrot (Daucus carota subsp. sativus) root was related to the expression of the lycopene ε‐cyclase gene DcLCYE. Catalytic activity analysis in Escherichia coli and gene function verification in transgenic carrot demonstrated that DcLCYE could alter the metabolic flow of carotenes. [ABSTRACT FROM AUTHOR]

The germination of carrot seeds is a complex regulatory process and the relationship between phytohormone and carrot seed germination is unclear. We performed morphological observation, transcriptome sequencing, phytohormone content determination, and gene expression profiles analysis. The results showed that the white hypocotyls of carrot seeds grew rapidly on the 3 d, and cotyledons unfold on the 8 d. A total of 745 differentially expressed genes (DEGs) related to plant hormone signal transduction were identified at different germination stages (3, 5, 8 d), and most of the genes were up-regulated obviously in the later stage. The content of GA3 reached its peak on the first day of germination, with a content of 7.12 ng/g FW, and showed a trend of first decreasing, then increasing and decreasing. And the trend of GA4 content change was similar to GA3 content from 2 d to 8 d. The contents of indole-3-acetic acid (IAA) and methyl jasmonate (MeJA) showed a gradual increasing trend, while the content of abscisic acid (ABA) gradually decreased. The results of RT-qPCR showed that DcGA3ox1 and DcAOC expressed decreased, while DcGA20ox2 and DcYUCCA increased in the whole process. These results provide potential new insights for the efficient production of carrots.. [ABSTRACT FROM AUTHOR]

The taproot of purple carrot accumulated rich anthocyanin, but non-purple carrot did not. MYB transcription factors (TFs) condition anthocyanin biosynthesis in many plants. Currently, genome-wide identification and evolution analysis of R2R3-MYB gene family and their roles involved in conditioning anthocyanin biosynthesis in carrot is still limited. In this study, a total of 146 carrot R2R3-MYB TFs were identified based on the carrot transcriptome and genome database and were classified into 19 subfamilies on the basis of R2R3-MYB domain. These R2R3-MYB genes were unevenly distributed among nine chromosomes, and Ka/Ks analysis suggested that they evolved under a purified selection. The anthocyanin-related S6 subfamily, which contains 7 MYB TFs, was isolated from R2R3-MYB TFs. The anthocyanin content of rhizodermis, cortex, and secondary phloem in 'Black nebula' cultivar reached the highest among the 3 solid purple carrot cultivars at 110 days after sowing, which was approximately 4.20- and 3.72-fold higher than that in the 'Deep purple' and 'Ziwei' cultivars, respectively. The expression level of 7 MYB genes in purple carrot was higher than that in non-purple carrot. Among them, DcMYB113 (DCAR_008994) was specifically expressed in rhizodermis, cortex, and secondary phloem tissues of 'Purple haze' cultivar, with the highest expression level of 10,223.77 compared with the control 'DPP' cultivar at 70 days after sowing. DcMYB7 (DCAR_010745) was detected in purple root tissue of 'DPP' cultivar and its expression level in rhizodermis, cortex, and secondary phloem was 3.23-fold higher than that of secondary xylem at 110 days after sowing. Our results should be useful for determining the precise role of S6 subfamily R2R3-MYB TFs participating in anthocyanin biosynthesis in carrot. [ABSTRACT FROM AUTHOR]

Studying the changes of carotenoids in the taproot of carrots under salt treatment is helpful to probe the salt stress response mechanism of carrots. The carotenoid concentration and the expression profiles of 10 carotenoid-related genes were determined in two carrot cultivars with different taproot colors. Under salt stress, the biosynthesis of carotenoids in the taproot of both 'KRD' and 'BHJS' was activated. RT-qPCR manifested that the expression levels of DcPSY1, DcPSY2, DcZDS1, DcCRT1 and DcCRT2 increased significantly in both 'KRD' and BHJS' under salt stress, but DcCHXE transcripts decreased and DcPDS transcripts maintained a basal level compared to that of the control. In the taproot of 'KRD', the expression level of DcLCYB, DcLCYE and DcCHXB1 climbed dramatically. However, there was no significant change in the taproot of 'BHJS'. The study showed that salt stress can stimulate the biosynthesis of carotenoids. The accumulation of lutein in the taproots of 'KRD' and 'BHJS' may be mainly attributed to the variation in DcLCYE and DcCHXB1 transcripts. The increase in β-carotene accumulation is speculated to increase salt tolerance. [ABSTRACT FROM AUTHOR]

Background: Carrot (Daucus carota L.), an important root vegetable, is very popular among consumers as its taproot is rich in various nutrients. Abiotic stresses, such as drought, salt, and low temperature, are the main factors that restrict the growth and development of carrots. Non-heme carotene hydroxylase (BCH) is a key regulatory enzyme in the β-branch of the carotenoid biosynthesis pathway, upstream of the abscisic acid (ABA) synthesis pathway. Results: In this study, we characterized a carrot BCH encoding gene, DcBCH1. The expression of DcBCH1 was induced by drought treatment. The overexpression of DcBCH1 in Arabidopsis thaliana resulted in enhanced tolerance to drought, as demonstrated by higher antioxidant capacity and lower malondialdehyde content after drought treatment. Under drought stress, the endogenous ABA level in transgenic A. thaliana was higher than that in wild-type (WT) plants. Additionally, the contents of lutein and β-carotene in transgenic A. thaliana were lower than those in WT, whereas the expression levels of most endogenous carotenogenic genes were significantly increased after drought treatment. Conclusions: DcBCH1 can increase the antioxidant capacity and promote endogenous ABA levels of plants by regulating the synthesis rate of carotenoids, thereby regulating the drought resistance of plants. These results will help to provide potential candidate genes for plant drought tolerance breeding. [ABSTRACT FROM AUTHOR]

Gibberellins (GAs) are a group of plant hormones that play important roles in various processes. Previous studies demonstrated that GA can increase the cellulose content and lignification of plant tissues. However, the effects of altered GA levels on carrot root development have not been fully characterized. In this study, carrot roots were treated with exogenous GA3, after which thickened cell walls were detected in the xylem area. Transcriptome sequencing data revealed the changes induced by GA3. A total of 5416 differentially expressed genes (DEGs) were identified, of which 3011 and 2405 were up- and down-regulated, respectively. The DEGs were enriched in metabolic pathways, with 236 DEGs related to the cell wall. Digital gene expression data and the verification by qRT-PCR indicated that exogenous GA can alter the expression of genes involved in cell wall synthesis, suggesting a potential role for GA in cell wall organization and modification. The results of this study provide novel insights into the GA functions influencing carrot root development. [ABSTRACT FROM AUTHOR]

Carotenoids are liposoluble pigments found in plant chromoplasts that are responsible for the yellow, orange, and red colors of carrot taproots. Drought is one of the main stress factors affecting carrot growth. Carotenoids play important roles in drought resistance in higher plants. In the present work, the carotenoid contents in three different-colored carrot cultivars, 'Kurodagosun' (orange), 'Benhongjinshi' (red), and 'Qitouhuang' (yellow), were determined by ultra-high-performance liquid chromatography (UPLC) after 15% polyethylene glycol (PEG) 6000 treatment. Real-time fluorescence quantitative PCR (RT-qPCR) was then used to determine the expression levels of carotenoid synthesis- and degradation-related genes. Increases in β-carotene content in 'Qitouhuang' taproots under drought stress were found to be related to the expression levels of DcPSY2 and DcLCYB. Increases in lutein and decreases in α-carotene content in 'Qitouhuang' and 'Kurodagosun' under PEG treatment may be related to the expression levels of DcCYP97A3, DcCHXE, and DcCHXB1. The expression levels of DcNCED1 and DcNCED2 in the three cultivars significantly increased, thus suggesting that NCED genes could respond to drought stress. Analysis of the growth status and carotenoid contents of carrots under PEG treatment indicated that the orange cultivar 'Kurodagosun' has better adaptability to drought stress than the other cultivars and that β-carotene and lutein may be involved in the stress resistance process of carrot. [ABSTRACT FROM AUTHOR]

Carrot is a root crop consumed worldwide and has great nutritional qualities. It is considered as one of the ten most important vegetable crops. Cytokinins are an essential class of the plant hormones that regulate many processes of plant growth. Till now, the effects of cytokinin, BAP, on lignin biosynthesis and related gene expression profiles in carrot taproot is unclear. In order to investigate the effect of applied BAP on lignin-related gene expression profiles, lignin accumulation, anatomical structures, and morphological characters in carrot taproots. Carrot roots were treated with different concentrations of BAP (0, 10, 20, and 30 mg L−1). The results showed that the application of BAP significantly increased plant length, shoot fresh weight, root fresh weight, and taproot diameter. In addition, BAP at 20 mg L−1 or 30 mg L−1 enhanced the average number of petioles. BAP treatment led to increased number and width of xylem vessels. The parenchyma cell numbers of pith were significantly induced in taproots treated with the BAP at a concentration of 30 mg L−1. BAP significantly upregulated most of the expression levels of lignin biosynthesis genes, caused elevated lignin accumulation in carrot taproots. Our results indicate that BAP may play important roles in growth development and lignification in carrot taproots. Our results provide a valuable database for more studies, which may focus on the regulation of root lignification via controlling cytokinin levels in carrot taproots. [ABSTRACT FROM AUTHOR]

Summary: Purple carrots, the original domesticated carrots, accumulate highly glycosylated and acylated anthocyanins in root and/or petiole. Previously, a quantitative trait locus (QTL) for root‐specific anthocyanin pigmentation was genetically mapped to chromosome 3 of carrot. In this study, an R2R3‐MYB gene, namely DcMYB113, was identified within this QTL region. DcMYB113 expressed in the root of 'Purple haze', a carrot cultivar with purple root and nonpurple petiole, but not in the roots of two carrot cultivars with a purple root and petiole (Deep purple and Cosmic purple) and orange carrot 'Kurodagosun', which appeared to be caused by variation in the promoter region. The function of DcMYB113 from 'Purple haze' was verified by transformation in 'Cosmic purple' and 'Kurodagosun', resulting in anthocyanin biosynthesis. Transgenic 'Kurodagosun' carrying DcMYB113 driven by the CaMV 35S promoter had a purple root and petiole, while transgenic 'Kurodagosun' expressing DcMYB113 driven by its own promoter had a purple root and nonpurple petiole, suggesting that root‐specific expression of DcMYB113 was determined by its promoter. DcMYB113 could activate the expression of DcbHLH3 and structural genes related to anthocyanin biosynthesis. DcUCGXT1 and DcSAT1, which were confirmed to be responsible for anthocyanins glycosylation and acylation, respectively, were also activated by DcMYB113. The WGCNA identified several genes co‐expressed with anthocyanin biosynthesis and the results indicated that DcMYB113 may regulate anthocyanin transport. Our findings provide insight into the molecular mechanism underlying root‐specific anthocyanin biosynthesis and further modification in carrot and even other root crops. [ABSTRACT FROM AUTHOR]

Carrot is an annual or biennial herbaceous plant of the Apiaceae family. Carrot is an important vegetable, and its fresh taproot, which contains rich nutrients, is the main edible part. In the life cycle of carrot, NAC family transcription factors (TFs) are involved in almost all physiological processes. The function of NAC TFs in carrot remains unclear. In this study, 73 NAC family TF members in carrot were identified and characterized using transcriptome and genome databases. These members were divided into 14 subfamilies. Multiple sequence alignment was performed, and the conserved domains, common motifs, phylogenetic tree, and interaction network of DcNAC proteins were predicted and analyzed. Results showed that the same group of NAC proteins of carrot had high similarity. Eight DcNAC genes were selected to detect their expression profiles under abiotic stress treatments. The expression levels of the selected DcNAC genes significantly increased under treatments with low temperature, high temperature, drought, and salt stress. Results provide potentially useful information for further analysis of the roles of DcNAC transcription factors in carrot. [ABSTRACT FROM AUTHOR]

Carotenoids are a group of natural pigments that are widely distributed in various plants. Carrots are plants rich in carotenoids and have fleshy roots with different colors. Carotenoid accumulation is a complex regulatory process with important guiding significance for carrot production. In this work, three carrot cultivars with different taproot colors, Hongxinqicun (orange), Benhongjinshi (red), and Tianzi (purple) were chosen as experimental materials to explore the molecular mechanism of carotenoid accumulation in carrot. Results showed that the three carotenoids, namely, α-carotene, β-carotene, and lutein, had accumulated in orange carrot cultivar Hongxinqicun. Lycopene was only detected in the taproots of Benhongjinshi. Lutein was the main carotenoid in Tianzi. Comparison of the carotenoid contents in different tissues of carrot showed that leaf blade was the tissue with the highest carotenoid accumulation. Expression analysis of carotenoid biosynthesis genes and its correlation with carotenoid accumulation confirmed the regulatory role of structural genes in carrots. The high expression of five lycopene synthesis-related genes, DcPSY2, DcPDS, DcZDS1, DcCRT1, DcCRT2, and low expression of DcLCYE may result in the lycopene accumulation in Benhongjinshi. However, the function of certain genes, such as DcPSY1 that was lowly expressed in red carrot, requires further investigation. Our results provided potential insights into the mechanism of carotenoid accumulation in three carrot cultivars with different taproot colors. [ABSTRACT FROM AUTHOR]

Celery (Apium graveolens L.) is one of the most important vegetables in the Apiaceae family, rich in nutrients and widely grown around the world. bZIP transcription factors family plays an important role in the transcription regulation of plant growth and development, as well as adaptation to the external environment. In this paper, 62 bZIP family transcription factors were screened and identified based on the whole genome sequence of celery. The bZIP proteins of celery and Arabidopsis thaliana were divided into 10 subfamilies according to the phylogenetic tree. Phylogenetic and evolutionary analysis showed that the number of bZIP family members gradually expanded from lower plants to higher plants during the long evolution process. Based on the homology of celery and A. thaliana bZIP genes, the interaction network between celery bZIP transcription factors and other proteins in the genome was constructed, and the correlation data of protein interaction were also obtained. The expression profiles of 12 selected AgbZIP genes were detected and analyzed under abiotic stress treatments and different tissues using RT-qPCR. The results showed that AgbZIP can respond to high temperature, low temperature, drought, and high salt stress. [ABSTRACT FROM AUTHOR]

Carrot is an important root vegetable crop with a variety of nutrients. As the main product of carrots, the growth and development of fleshy roots directly determine the yield and quality of carrots. However, molecular mechanism underlying the carrot root formation and expansion is still limited. In our study, isobaric tags for relative and absolute quantification (iTRAQ) was utilized to explore the differentially expressed proteins (DEPs) during different developmental stages of carrot roots. Overall, 2,845 proteins were detected, of which 118 were significantly expressed in all three stages. DEPs that participated in several growth metabolisms were identified, including energy metabolism, defense metabolism, cell growth and shape regulation. Among them, two expansin proteins were obtained. A total of 30 expansin genes were identified based on the carrot genome database. Structure analysis showed that carrot expansin gene family was relatively conserved. Based on the expression analysis, we found that the expression profile of expansins genes was up-regulated during the vigorous growing period of carrot root. Furthermore, there was a consistent relationship between the expression patterns of mRNA and protein. The results indicated that expansin proteins might play important roles during root development in carrot. Our work provided useful information for understanding molecular mechanism of carrot root development. [ABSTRACT FROM AUTHOR]

The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot. Purifying selection also contributed to the evolution of carrot homeobox genes. In Gene Ontology (GO) analysis, most members of the HD-ZIP III and IV subfamilies were found to have a lipid binding (GO:0008289) term. Most HD-ZIP III and IV genes also harbored a steroidogenic acute regulatory protein-related lipid transfer (START) domain. These results suggested that the HD-ZIP III and IV subfamilies might be related to lipid transfer. Transcriptome and quantitative real-time PCR (RT-qPCR) data indicated that members of the WOX and KNOX subfamilies were likely implicated in carrot root development. Our study provided a useful basis for further studies on the complexity and function of the homeobox gene family in carrot. [ABSTRACT FROM AUTHOR]

Key message: Hypoxia enhances lignification of carrot root.Abstract: Hypoxia stress was thought to be one of the major abiotic stresses that inhibiting the growth and development of higher plants. The genes encoding the plant alcohol dehydrogenase (ADH-P) were induced when suffering hypoxia. To investigate the impact of hypoxia on the carrot root growth, carrot plants were cultivated in the hydroponics with or without aeration. Morphological characteristics, anatomical structure, lignin content, and the expression profiles of DcADH-P genes and lignin biosynthesis-related genes were measured. Six DcADH-P genes were identified from the carrot genome. The expression profiles of only three (DcADH-P1, DcADH-P2, and DcADH-P3) genes could be detected and the other three (DcADH-P4, DcADH-P5, and DcADH-P6) could not be detected when carrot cultivated in the solution without aeration. In addition, carrot roots had more lignin content, aerenchyma and less fresh weight when cultivated in the solution without aeration. These results suggested that hypoxia could enhance the lignification and affect anatomical structure of the carrot root. However, the expression levels of the genes related to lignin biosynthesis were down-regulated under the hypoxia. The enhancement of lignification may be the consequence of the structure changes in the carrot root. Our work was potentially helpful for studying the effect of hypoxia on carrot growth and may provide useful information for carrot hydroponics. [ABSTRACT FROM AUTHOR]

The male-sterile carrot is an effective material for carrot breeding. The atp6 gene is involved in carrot fertility. However, the differences in lengths, copies, and expression profiles of the atp6 gene in fertile and male-sterile lines of carrot are unclear. In this study, one copy atp6 gene was found in the mtDNAs of ‘Kuroda’ (fertility, 954 bp) and ‘Wuye-BY’ (male sterility, 819 bp) carrot lines, while two copies atp6 genes (Wuye-L and Wuye-D, 954 bp and 819 bp, respectively) were found in the mtDNA of ‘Wuye’ (fertility). Two putative conserved domains have been detected in the carrot atp6 protein. Evolutionary analysis showed that the atp6 protein sequences of Wuye-L and Kuroda were clustered in the same branch, while Wuye-D and Wuye-BY were clustered in the same branch. The atp6 gene was higher expressed in the flowers of ‘Kuroda’ and ‘Wuye’ (Wuye-L), while lower expressed in ‘Wuye-BY’ and ‘Wuye’ (Wuye-D). [ABSTRACT FROM AUTHOR]

Gibberellins (GAs) are important growth regulators involved in plant development processes. However, limited information is known about the relationship between GA and xylogenesis in carrots. In this study, carrot roots were treated with GA. The effects of applied GA on root growth, xylem development, and lignin accumulation were then investigated. Results indicated that GA treatment dose-dependently inhibited carrot root growth. The cell wall significantly thickened in the xylem parenchyma. Autofluorescence analysis with ultraviolet (UV) excitation indicated that these cells became lignified because of long-term GA treatment. Moreover, lignin content increased in the roots, and the transcripts of lignin biosynthesis genes were altered in response to applied GA. Our data indicate that GA may play important roles in xylem growth and lignification in carrot roots. Further studies shall focus on regulating plant lignification, which may be achieved by modifying GA levels within plant tissues. [ABSTRACT FROM AUTHOR]

Purple carrots accumulate abundant cyanidin-based anthocyanins in taproots. UDP-glucose: sinapic acid glucosyltransferase (USAGT) can transfer the glucose moiety to the carboxyl group of sinapic acid thereby forming the ester bond between the carboxyl-C and the C1 of glucose (1-O-sinapoylglucose). 1-O-sinapoylglucose can serve as an acyl donor in acylation of anthocyanins and generate cyanidin 3-xylosyl (sinapoylglucosyl) galactoside in purple carrots. This final product helps stabilize the accumulation of anthocyanins. In this study, a gene named DcUSAGT1 encoding USAGT was cloned from ‘Deep purple’ carrot taproots. Enzymatic activity was determined using high performance liquid chromatography (HPLC). The optimal temperature and pH value were 30°C and 7.0, respectively. Kinetic analysis suggested a Km (sinapic acid) of 0.59 mM. Expression profiles of DcUSAGT1 showed high expression levels in the taproots of all the three purple carrot cultivars but low expression levels in those of non-purple carrot cultivars. The USAGT activity of different carrots in vitro indicated that crude enzyme extracted from the purple carrot taproots rather than non-purple carrot taproots exhibited USAGT activity. These results indicated that DcUSAGT1 may influence anthocyanin biosynthesis of purple carrot taproots. [ABSTRACT FROM AUTHOR]

AP2/ERF is a large transcription factor family that regulates plant physiological processes, such as plant development and stress response. Carrot ( Daucus carota L.) is an important economical crop with a genome size of 480 Mb; the draft genome sequencing of this crop has been completed by our group. However, little is known about the AP2/ERF factors in carrot. In this study, a total of 267 putative AP2/ERF factors were identified from the whole-genome sequence of carrot. These AP2/ERF proteins were phylogenetically clustered into five subfamilies based on their similarity to the amino acid sequences from Arabidopsis. The distribution and comparative genome analysis of the AP2/ERF factors among plants showed the AP2/ERF factors had expansion during the evolutionary process, and the AP2 domain was highly conserved during evolution. The number of AP2/ERF factors in land plants expanded during their evolution. A total of 60 orthologous and 145 coorthologous AP2/ERF gene pairs between carrot and Arabidopsis were identified, and the interaction network of orthologous genes was constructed. The expression patterns of eight AP2/ERF family genes from each subfamily (DREB, ERF, AP2, and RAV) were related to abiotic stresses. Yeast one-hybrid and β-galactosidase activity assays confirmed the DRE and GCC box-binding activities of DREB subfamily genes. This study is the first to identify and characterize the AP2/ERF transcription factors in carrot using whole-genome analysis, and the findings may serve as references for future functional research on the transcription factors in carrot. [ABSTRACT FROM AUTHOR]

Cytokinins have been implicated in normal plant growth and development. These bioactive molecules are essential for cell production and expansion in higher plants. Carrot is an Apiaceae vegetable with great value and undergoes significant size changes over the process of plant growth. However, cytokinin accumulation and its potential roles in carrot growth have not been elucidated. To address this problem, carrot plants at five stages were collected, and morphological and anatomical characteristics and expression profiles of cytokinin-related genes were determined. During carrot growth and development, cytokinin levels were the highest at the second stage in the roots, whereas relatively stable levels were observed in the petioles and leaves. DcCYP735A2 showed high expression at stage 2 in the roots, which may contribute largely to the higher cytokinin level at this stage. However, expression of most metabolic genes did not follow a pattern similar to that of cytokinin accumulation, indicating that cytokinin biosynthesis was regulated through a complex network. Genes involved in cytokinin signal perception and transduction were also integrated to normal plant growth and development. The results from the present work suggested that cytokinins may regulate plant growth in a stage-dependent manner. Our work would shed novel insights into cytokinin accumulation and its potential roles during carrot growth. Further studies regarding carrot cytokinins may be achieved by modification of the genes involved in cytokinin biosynthesis, inactivation, and perception. [ABSTRACT FROM AUTHOR]

Carrot, a biennial herb of the Apiaceae family, is among the most important vegetable crops in the world. In this study, nine candidate reference genes (GAPDH, ACTIN, eIF-4α, PP2A, SAND, TIP41, UBQ, EF-1α, and TUB) were cloned from carrot. Carrot plants were subjected to abiotic stresses (heat, cold, salt, and drought) and hormone stimuli (gibberellin, salicylic acid, methyl jasmonate, and abscisic acid). The expression profiles of the candidate reference genes were evaluated in three technical and biological replicates. Real-time qPCR data analyses were performed using three commonly used Excel-based applets namely, BestKeeper, geNorm, and NormFinder. ACTIN and TUB were the most stable genes identified among all sample groups, but individual analysis revealed changes in their expression profiles. GAPDH displayed the maximum stability for most of single stresses. To further validate the suitability of the reference genes identified in this study, the expression profile of DcDREB-A1 gene (homolog of AtDREB-A1 gene of Arabidophsis) was studied in carrot. The appropriate reference genes were selected that showed stable expression under the different experimental conditions. [ABSTRACT FROM AUTHOR]

Little is known about the factors regulating carotenoid biosynthesis in roots. In this study, we characterized DCAR_032551, the candidate gene of the Y locus responsible for the transition of root color from ancestral white to yellow during carrot (Daucus carota) domestication. We show that DCAR_032551 encodes a REPRESSOR OF PHOTOSYNTHETIC GENES (RPGE) protein, named DcRPGE1. DcRPGE1 from wild carrot (DcRPGE1W) is a repressor of carotenoid biosynthesis. Specifically, DcRPGE1W physically interacts with DcAPRR2, an ARABIDOPSIS PSEUDO-RESPONSE REGULATOR2 (APRR2)-like transcription factor. Through this interaction, DcRPGE1W suppresses DcAPRR2-mediated transcriptional activation of the key carotenogenic genes phytoene synthase 1 (DcPSY1), DcPSY2, and lycopene ε-cyclase (DcLCYE), which strongly decreases carotenoid biosynthesis. We also demonstrate that the DcRPGE1W–DcAPRR2 interaction prevents DcAPRR2 from binding to the RGATTY elements in the promoter regions of DcPSY1, DcPSY2, and DcLCYE. Additionally, we identified a mutation in the DcRPGE1 coding region of yellow and orange carrots that leads to the generation of alternatively spliced transcripts encoding truncated DcRPGE1 proteins unable to interact with DcAPRR2, thereby failing to suppress carotenoid biosynthesis. These findings provide insights into the transcriptional regulation of carotenoid biosynthesis and offer potential target genes for enhancing carotenoid accumulation in crop plants. The carrot Y locus encodes a protein that interacts with transcription factor DcAPRR2, thereby inhibiting DcAPRR2-mediated activation of key carotenogenic genes and repressing carotenoid biosynthesis. [ABSTRACT FROM AUTHOR]

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The carrot is an important horticultural crop of the Apiaceae family, possessing considerable nutritional and economic value. Unfortunately, the decline in the postharvest quality has resulted in a decrease in the desirability of carrots and further food wastage. Nitric oxide (NO) plays a crucial role in alleviating the senescence and reducing losses of postharvest horticultural products, but its impact on the postharvest quality of carrots has not been reported. In this study, the effects of treatment with ddH 2 O, varying concentrations of sodium nitroprusside (SNP), and carboxy-PTIO (cPTIO) on the whiteness index, weight loss, and sensory scoring were evaluated, and a concentration of 1.5 mM SNP treatment preserved the appearance quality of postharvest carrots. Further analysis revealed that SNP treatment led to an increase in endogenous NO content by promoting nitrate reductase activity, which subsequently enhanced the expression of DcPSY1 , DcPDS1 , DcZDS1 , DcCRTISO1 , and DcLCYB1 and increased the levels of total carotenoid, α-carotenoid, and β-carotenoid. The alternation of carotenoids both increased abscisic acid (ABA) level by promoting the expression of ABA biosynthesis genes, but also hindered the generation of hydrogen peroxide and superoxide anion. Meanwhile, the expression of lignin biosynthesis genes was downregulated in SNP treatment group, resulting in postharvest carrots with lower lignin content and a lower degree of cell lignification. Overall, our findings provide a theoretical basis for the application of NO in the postharvest preservation of carrots and shed light on the role of NO in regulating the synthesis mechanisms of carotenoids and lignin in postharvest carrots. • 1.5 mM SNP promoted endogenous NO level by increasing NR activity. • SNP enhanced the accumulation of total carotenoid, α-carotenoid, and β-carotenoid. • SNP inhibited the lignification by promoting ABA synthesis and inhibiting ROS generation. • SNP preserved the appearance quality of postharvest carrots. [ABSTRACT FROM AUTHOR]

• A total of 104 MADS-box genes were obtained from the genome of carrot. • 48 and 56 members belonged to Type Ⅰ and Type Ⅱ, respectively. • Yeast two-hybrid assay showed that some DcMDAS-box proteins had interactions. • The expression profiles of DcMADS-box genes had varietal and stage specificity. MADS-box is the important transcription factor involved in the process of nutritional and reproductive growth of plants. To explore the information of MADS-box transcription factors in carrots (Daucus carota L.), we conducted a genome-wide identification and characteristic analysis of MADS-box in carrot. A total of 104 MADS-box factors were identified, and 48 Type Ⅰ MADS-box factors were classified into three subfamilies, Mα, Mβ, and Mγ. Among the 56 type Ⅱ MADS-box factors, 51 MADS-box factors belonged to MIKCC and 5 factors belonged to MIKC*. Subcellular localization prediction indicated that most DcMADS-box proteins were localized in the nuclear. A total of 90 DcMADS-box genes were distributed on all 9 chromosomes, and 19 tandem duplication gene pairs and 20 segmental duplication gene pairs were identified. The DcMADS-box promoter contained a variety of cis -acting regulatory elements, such as light responsiveness elements, low-temperature responsiveness elements, and hormone responsiveness elements. The results of protein interaction prediction and yeast two-hybrid assay indicated that DcMDAS-box proteins related to flowering, such as DcMADS004 and DcMADS079 can interact with DcMADS012. In addition, we found that the expression profiles of floral organ-related genes showed varietal differences and stage specificity in the three stages (early flower bud stage, middle flower bud stage, and full bloom stage) of 'Kurodagosun' (KRD) and 'Deep purple' (DPP). These results provide a potential theoretical basis for exploring the molecular mechanisms of carrot flower organ development. [ABSTRACT FROM AUTHOR]

The phytochrome-interacting factor (PIF) subfamily of basic helix-loop-helix (bHLH) transcription factors plays a critical role in plant growth and development. However, there has been no detailed report on the PIFs in carrot. In this study, we present the identification and characterization of DcPIF gene family in carrot (Daucus carota L.). Phylogenetic analysis indicated that PIFs from carrot and other five plant species could be divided into four groups supported by similar gene structure and motif analysis. Expression profiles showed that all DcPIF genes were tissue-specific and could be induced by drought or abscisic acid (ABA) treatment except DcPIF7.1 , among which DcPIF3 was the most responsive. The DcPIF3 -overexpressed Arabidopsis plants exhibited more tolerance to drought stress, with higher antioxidant capacity and lower malondialdehyde content after drought treatment than wild type plants. Further stress tolerance assays revealed that DcPIF3 plays a positive role in drought stress by increasing endogenous ABA level and promoting the expression of ABA-related genes. Our results can enrich the understanding of DcPIF family genes and lay a foundation for further investigation of DcPIF3 function to defend against drought stress in carrot. • DcPIF gene family, the phytochrome-interacting factor of carrot, was identified and characterized. • DcPIF3 improves drought tolerance in transgenic Arabidopsis with higher reactive oxygen species scavenging capability. • DcPIF3 increases endogenous ABA level by regulating the expression of ABA biosynthesis and catabolism genes. [ABSTRACT FROM AUTHOR]

Ascorbic acid (AsA), also known as vitamin C, is an essential nutrient in fruits and vegetables. The fleshy root of carrot ( Daucus carota L.) is a good source of AsA for humans. However, the metabolic pathways and molecular mechanisms involved in the control of AsA content during root development in carrot have not been elucidated. To gain insights into the regulation of AsA accumulation and to identify the key genes involved in the AsA metabolism, we cloned and analyzed the expression of 21 related genes during carrot root development. The results indicate that AsA accumulation in the carrot root is regulated by intricate pathways, of which the l - galactose pathway may be the major pathway for AsA biosynthesis. Transcript levels of the genes encoding l -galactose-1-phosphate phosphatase and l -galactono-1,4-lactone dehydrogenase were strongly correlated with AsA levels during root development. Data from this research may be used to assist breeding for improved nutrition, quality, and stress tolerance in carrots. [ABSTRACT FROM AUTHOR]

• DcABF3, an ABA-responsive element-binding transcription factor, was cloned and functionally characterized. • DcABF3 alters drought tolerance by increasing stomatal density in Arabidopsis. • DcABF3 reduces ABA sensitivity in transgenic Arabidopsis. Abscisic acid-responsive element (ABRE)-binding factors (ABFs) are important transcription factors involved in various physiological processes in plants. Stomata are micro channels for water and gas exchange of plants. Previous researches have demonstrated that ABFs can modulate the stomatal development in some plants. However, little is known about stomata-related functions of ABFs in carrots. In our study, DcABF3 , a gene encoding for ABF transcription factor, was isolated from carrot. The open reading frame of DcABF3 was 1329 bp, encoding 442 amino acids. Expression profiles of DcABF3 indicated that DcABF3 can respond to drought, salt or ABA treatment in carrots. Overexpressing DcABF3 in Arabidopsis led to the increase of stomatal density which caused severe water loss. Expression assay indicated that overexpression of DcABF3 caused high expression of stomatal development-related transcription factor genes, SPCH , FAMA , MUTE and SCRM s. Increased antioxidant enzyme activities and higher expression levels of stress-related genes were also found in transgenic lines after water deficit treatment. Changes in expression of ABA synthesis-related genes and AtABI s indicated the potential role of DcABF3 in ABA signaling pathway. Under the treatment of exogenous ABA, DcABF3 -overexpression Arabidopsis seedlings exhibited increased root length and germination rate. Our findings demonstrated that heterologous overexpression of DcABF3 positively affected stomatal development and also reduced ABA sensitivity in transgenic Arabidopsis. [ABSTRACT FROM AUTHOR]

• A total of 111 putative NAC TFs were found and identified based on celery transcriptome and genome database. • The AgNAC TFs were classified into 18 subfamilies and their physicochemical properties were preliminary analyzed. • Expression profiles of selected AgNAC genes in response to abiotic stress were detected. In plants, NAC (NAM, ATAF, CUC) is a class of transcription factors (TFs) involved in growth regulation and is associated with abiotic stress, morphogenesis, and metabolism. Celery (Apium graveolens L.) is an important leafy vegetable and its yield and quality are considerably influenced by environmental factors. Currently, the characterization of NAC genes in celery is still limited. In this study, a total of 111 putative NAC TFs were determined based on the celery transcriptome and genome database. They were divided into 18 subfamilies on the basis of their NAC domain. NAC TFs in celery account for a moderate number compared with other species, similar to that in carrot. Real-time quantitative PCR (RT-qPCR) showed that some AgNAC genes were differentially expressed under adverse conditions (heat, cold, drought, and salt). AgNAC63 (ortholog of ANAC072 / RD26) was highly induced by heat, cold, and salt conditions. The expression levels of AgNAC47 in leaf blades were 105.25- and 123.14-fold those of petioles and roots, respectively. AgNAC63 and AgNAC47 showed significant tissue specificity, high expression in leaves, and varying degrees of response under the four treatments. This study provides a basis for the improved investigation of the structure and function of AgNAC TFs and celery stress resistance. [ABSTRACT FROM AUTHOR]

• A DREB-binding transcription factor from Daucus carota was characterized. • Overexpression of DcDREB1A in Arabidopsis increases antioxidant capacity. • The accumulation of lignin was modulated by DcDREB1A. • DcDREB1A as positive regulator involved in regulation of plants tolerance to drought. Carrot (Daucus carota L.) is an important root vegetable of Apiaceae, whose growth and production are negatively affected by abiotic stress. Dehydration-responsive element-binding protein (DREB) transcription factors usually play significant roles in the responses of plants to abiotic stress. However, knowledge on the functions of DREB transcription factors in carrots remains limited. In this study, the functional characterization of a DREB gene, DcDREB1A , cloned from carrot was reported. DcDREB1A was found to be a nuclear protein that can specifically bind to DRE element. Under drought treatment, DcDREB1A overexpression in transgenic plants resulted in increased superoxide dismutase (SOD) and peroxidase (POD) activities and decreased size of stomata apertures. Moreover, transgenic plants accumulated an increased amount of lignin and exhibited higher expression levels of lignin biosynthesis gene compared with wild-type plants. Overall, our findings revealed that DcDREB1A was involved in the regulation of plant tolerance to drought. DcDREB1A served as a positive regulator by regulating the activities of reactive oxygen species (ROS)-scavenging enzymes (SOD and POD) to maintain ROS homeostasis in cells, reducing stomata apertures and density, modulating lignin synthesis to control water loss, and inducing the expression of stress-responsive genes. [ABSTRACT FROM AUTHOR]