Anthocyanin glucosylation mediated by a glycoside hydrolase family 3 protein in purple carrot.

Purple carrot accumulates anthocyanins modified with galactose, xylose, glucose, and sinapic acid. Most of the genes associated with anthocyanin biosynthesis have been identified, except for the glucosyltransferase genes involved in the step before the acylation in purple carrot. Anthocyanins are commonly glycosylated in reactions catalyzed by UDP-sugar-dependent glycosyltransferases (UGTs). Although many studies have been conducted on UGTs, the glucosylation of carrot anthocyanins remains unknown. Acyl-glucose-dependent glucosyltransferase activity modifying cyanidin 3-xylosylgalactoside was detected in the crude protein extract prepared from purple carrot cultured cells. In addition, the corresponding enzyme was purified. The cDNA encoding this glucosyltransferase was isolated based on the partial amino acid sequence of the purified protein. The recombinant protein produced in Nicotiana benthamiana leaves via agroinfiltration exhibited anthocyanin glucosyltransferase activity. This glucosyltransferase belongs to the glycoside hydrolase family 3 (GH3). The expression pattern of the gene encoding this GH3-type anthocyanin glucosyltransferase was consistent with anthocyanin accumulation in carrot tissues and cultured cells.

Exogenous CaCl2 reduces the oxidative cleavage of carotenoids in shredded carrots by targeting CAMTA4-mediated transcriptional repression of carotenoid degradation pathway.

Carotenoid oxidative cleavage is a significant factor contributing to the color changes of shredded carrots and treatment with calcium chloride (CaCl2, 1% w/v) has been observed to alleviate the whitening symptom and color loss. However, the specific mechanism by which CaCl2 treatment suppresses carotenoid degradation remains unclear. In this study, the effect of CaCl2 and EGTA (calcium ion chelating agent) treatment on carotenoid biosynthesis and degradation in shredded carrots and the mechanism involved was investigated. CaCl2 treatment promoted the expression and activity of carotenoid biosynthetic enzyme (phytoene synthase, PSY), but inhibited the increases of the degradative enzyme activity of carotenoid cleavage dioxygenase (CCD) and down-regulated the corresponding transcripts, thus delayed the degradation of total carotenoid and maintaining higher levels of major carotenoid compounds including ß-carotene, α-carotene, lycopene, and lutein in shredded carrots during storage. However, EGTA treatment promoted the gene expression and enzyme activity of CCD and increased the degradation of carotenoid compounds in shredded carrots during storage. Furthermore, the CaCl2 treatment induced DcCAMTA4, identified as a calcium decoder in shredded carrots, which, in turn, suppressed the expressions of DcCCD1 and DcCCD4 by interacting with their promoters. The transient overexpression of DcCAMTA4 in tobacco leaves led to reduced expression of NtCCD1 and NtCCD4, maintaining a higher content of carotenoids. Thus, CaCl2 alleviated the oxidative cleavage of carotenoids in shredded carrots through the DcCAMTA4-mediated carotenoid degradation pathway.

Pollen-mediated gene flow from wild carrots (Daucus carota L. subsp. carota) affects the production of commercial carrot seeds (Daucus carota L. subsp. sativus) internationally and in New Zealand in the context of climate change: A systematic review.

Climate change will impact the carrot seed industry globally. One adaptation strategy to limit climatic impacts on the production of commercial carrot seeds is geographical shift. However, production must be shifted to climate-optimal places that are free from weeds such as wild carrots to avoid genetic contamination via hybridization. The process of gene flow between wild and cultivated carrots is critical to enable management of wild carrots in the face of climate change. This review systematically assesses the resilience of wild carrots to climate change and their impact on commercial carrot seed production globally with a focus on New Zealand as a major carrot seed producer. The literature was critically analyzed based on three specific components: i) resilience of wild carrots to climate change ii) genetic contamination between wild and cultivated carrots, and iii) management of wild carrots. The majority of the articles were published between 2013 and 2023 (64.71 %), and most of these studies were conducted in Europe (37.26 %) and North America (27.45 %). Country-wise analysis demonstrated that the majority of the studies were carried out in the United States (23.53 %) and the Netherlands (11.77 %). There was limited research conducted in other regions, especially in Oceania (1.96 %). Spatial distribution analysis revealed that the wild carrot was reported in around 100 countries. In New Zealand the North Island has a higher incidence of wild carrot invasion than the South Island. The findings indicated that the wild carrot is becoming more adaptable to climate change, compromising the genetic purity of cultivated carrots due to pollen flow from wild to cultivated carrots. Therefore, ongoing research will be helpful in developing sustainable weed management strategies and predicting potential geographical invasiveness. This study provides a guide for scientists, policymakers, industrialists, and farmers to control wild carrots and produce genetically pure commercial seeds amid climate change.

The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot.

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.

Genome-wide analysis of plant specific YABBY transcription factor gene family in carrot (Dacus carota) and its comparison with Arabidopsis.

YABBY gene family is a plant-specific transcription factor with DNA binding domain involved in various functions i.e. regulation of style, length of flowers, and polarity development of lateral organs in flowering plants. Computational methods were utilized to identify members of the YABBY gene family, with Carrot (Daucus carota) 's genome as a foundational reference. The structure of genes, location of the chromosomes, protein motifs and phylogenetic investigation, syntony and transcriptomic analysis, and miRNA targets were analyzed to unmask the hidden structural and functional characteristics YABBY gene family in Carrots. In the following research, it has been concluded that 11 specific YABBY genes irregularly dispersed on all 9 chromosomes and proteins assembled into five subgroups i.e. AtINO, AtCRC, AtYAB5, AtAFO, and AtYAB2, which were created on the well-known classification of Arabidopsis. The wide ranges of YABBY genes in carrots were dispersed due to segmental duplication, which was detected as prevalent when equated to tandem duplication. Transcriptomic analysis showed that one of the DcYABBY genes was highly expressed during anthocyanin pigmentation in carrot taproots. The cis-regulatory elements (CREs) analysis unveiled elements that particularly respond to light, cell cycle regulation, drought induce ability, ABA hormone, seed, and meristem expression. Furthermore, a relative study among Carrot and Arabidopsis genes of the YABBY family indicated 5 sub-families sharing common characteristics. The comprehensive evaluation of YABBY genes in the genome provides a direction for the cloning and understanding of their functional properties in carrots. Our investigations revealed genome-wide distribution and role of YABBY genes in the carrots with best-fit comparison to Arabidopsis thaliana.

An SpG-Cas9-based cytosine base editor expands the scope of genome editing in carrot plants.

KEY MESSAGE: SpG Cas9 significantly expands the genome editing scope in carrot with NGN PAM recognition.

Transcriptome Sequencing Reveals the Mechanism of Auxin Regulation during Root Expansion in Carrot.

Carrot is an important vegetable with roots as the edible organ. A complex regulatory network controls root growth, in which auxin is one of the key players. To clarify the molecular mechanism on auxin regulating carrot root expansion, the growth process and the indole-3-acetic acid (IAA) content in the roots were measured in this experiment. It was found that the rapid expansion period of the root was from 34 to 41 days after sowing and the IAA content was the highest during this period. The root growth then slowed down and the IAA levels decreased. Using the transcriptome sequencing database, we analyzed the expression of IAA-metabolism-related genes and found that the expression of most of the IAA synthesis genes, catabolism genes, and genes related to signal transduction was consistent with the changes in IAA content during root expansion. Among them, a total of 31 differentially expressed genes (DEGs) were identified, including 10 IAA synthesis genes, 8 degradation genes, and 13 genes related to signal transduction. Analysis of the correlations between the DEGs and IAA levels showed that the following genes were closely related to root development: three synthesis genes, YUCCA10 (DCAR_012429), TAR2 (DCAR_026162), and AMI1 (DCAR_003244); two degradation genes, LPD1 (DCAR_023341) and AACT1 (DCAR_010070); and five genes related to signal transduction, IAA22 (DCAR_012516), IAA13 (DCAR_012591), IAA27 (DCAR_023070), IAA14 (DCAR_027269), and IAA7 (DCAR_030713). These results provide a reference for future studies on the mechanism of root expansion in carrots.

Linkage mapping of root shape traits in two carrot populations.

This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.

Genetic parameters estimate for plant characters of a particular carrot population in two different agroecologic cultivation systems / Parâmetros genéticos estimados para caracteres de planta de uma população particular de cenoura em dois sistemas de cultivo agroecológico diferentes

Carrots are among the most planted vegetables in Brazil, which represents importance in the national market. This crop can be grown in conventional and agroecological systems, and studies to improve productivity, disease resistance and root quality in agroecological cropping systems are important. The aim of the present work was to estimate genetic parameters that provide a breeding strategy in the search for the development of new varieties of carrot adapted to the conditions of Distrito Federal's agroecology cultivation. Considering data from tests performed in areas of agroecology cultivation (Natural Agriculture-NA and Organic Agriculture-OA), the following characteristics were evaluated: incidence of leaf blight-LB, incidence of root cracking-CRACK, root length-COMP, format of root tip-TP, format of root shoulder-TO, measure of the color of the a* xylem parameter-a*X, measure of the color of the a* phloem parameter-a*F. Traits were evaluated in 100 half-sib progenies derived from Brasília cultivar, using a completely randomized block design. For the characters COMP, a*X, a*F, TP and TO, the treatment X environment interaction was significant according to the results from test F. The values of the individual variance analyses presented significant effect for the following characteristics: COMP, a*X, TP, TO, LB for NA system, and COMP, a*X, a*F, TP for OA system. In NA system, the values of heritability estimates-ha² for the plant characters fluctuated from 65.66 to 25.52% and, in the OA system, the ha² of the characters a*X, was 81.13%. Estimates of genetic gain per cycle for the characters a*X and a*F were lower in NA system than the estimates observed in OA system.

A cenoura está entre as hortaliças mais plantadas no Brasil, o que representa importância no mercado nacional. Essa cultura pode ser cultivada em sistemas convencionais e agroecológicos, sendo importante o desenvolvimento de estudos para melhorar características de produtividade, resistência a doenças e qualidade de raiz em sistemas com base agroecológica de cultivo. O objetivo do presente trabalho foi estimar parâmetros genéticos que fornecem uma estratégia de melhoramento na busca pelo desenvolvimento de novas variedades de cenoura adaptadas às condições do cultivo agroecológico do Distrito Federal. Considerando dados de testes realizados em áreas de cultivo agroecológico (Agricultura Natural - NA e Agricultura Orgânica - OA), foram avaliadas as seguintes características: incidência de queima das folhas - LB, incidência de rachadura radicular - RACH, comprimento de raiz - COMP, formato de raiz -TP, formato do ombro -TO, medida da cor do parâmetro a * do xilema ­ a*X, medida da cor do parâmetro a *do floema ­ a*F. As características foram avaliadas em 100 progênies de meios-irmãos derivadas da cultivar Brasília, usando um delineamento de blocos inteiramente casualizados. Para os caracteres COMP, a*X, a*F, TP e TO, a interação tratamento X ambiente foi significativa de acordo com os resultados do teste F. Os valores das análises de variância individuais apresentaram efeito significativo para as seguintes características: COMP, a*X, TP, TO, LB para o sistema NA e COMP, a*X, um a*F, TP para o sistema OA. No sistema NA, os valores de estimativa de herdabilidade - ha² para os caracteres da planta variaram de 65,66 a 25,52% e, no sistema OA, o ha² da característica a*X foi de 81,13%. As estimativas de ganho genético por ciclo para os caracteres a*X e a*F foram menores no sistema NA do que as estimativas observadas no sistema OA.

Daucus carota as a novel model to evaluate the effect of light on carotenogenic gene expression

Carotenoids are synthesized in prokaryotic and eukaryotic organisms. In plants and algae, these lipophilic molecules possess antioxidant properties acting as reactive oxygen species scavengers and exert functional roles in hormone synthesis, photosynthesis, photomorphogenesis and in photoprotection. During the past decade almost all carotenogenic genes have been identified as a result of molecular, genetic and biochemical approaches utilizing Arabidopsis thaliana as the model system. Studies carried out in leaves and fruits of A. thaliana and tomato determined that light regulates carotenoid biosynthesis preferentially through the modulation of carotenogenic gene transcription. In this work we showed for the first time that light induces accumulation of psy 1, pds and zds2 transcripts in leaves of Daucus carota (carrot), a novel plant model. In addition, modified roots of carrots exposed to light accumulate zdsl, whereas the pds gene is highly repressed, suggesting that some carotenogenic genes, which are expressed in roots, are regulated by light. Additionally, light negatively regulates the development of the modified carrot root in a reversible manner. Therefore, this suggests that light affects normal growth and carotenogenic gene expression in the modified root of carrot plants. The molecular insight gained into the light-regulated expression of carotenoid genes in this and other model systems will facilitate our understanding of the regulation of carotenoid biosynthesis to improve the prospects for the metabolic engineering of carotenoid production in plants.

Path analysis suggests phytoene accumulation is the key step limiting the carotenoid pathway in white carrot roots

Two F2 carrot (Daucus carota L.) populations (orange rooted Brasilia x very dark orange rooted High Carotene Mass - HCM cross and the dark orange rooted cultivated variety B493 x white rooted wild carrot Queen Anne's Lace - QAL cross) with very unrelated genetic backgrounds were used to investigate intrinsic factors limiting carotenoid accumulation in carrots by applying phenotypic correlation and path analysis to study the relationships between major root carotenes, root color and several other morphological traits. Most of the correlations between traits were close and agreed in sign between the two populations. Root weight had a moderate to highly significant positive correlation with leaf length, root length and top and middle root diameter. Although phenotypic correlations failed to identify the order of the substrates and products in the carotenoid pathway the correct order of substrates and products (phytoene -> zeta-carotene -> lycopene) was identified in the causal diagram of beta-carotene for the Brasilia x HCM population. Path analysis of beta-carotene synthesis in the B493 x QAL population suggested that selection for root carotenes had little effect on plant morphological traits. Causal model of beta-carotene and lycopene in the B493 x QAL population suggested that phytoene synthesis is the key step limiting the carotenoid pathway in white carrots. Path analysis, first presented by Sewall Wright to study quantitative traits, appears to be a powerful statistical approach for the identification of key compounds in complex pathways.

Genetic parameter estimates and efficiency of three selection procedures in carrot breeding, variety Campinas

The potential for genetic breeding of the carrot variety "Campinas" was assessed through estimates of the genetic-statistical parameters of 16 traits of agronomic importance. The parameters were obtained from 102 half-sib progenies, harvested in a seed production field. Two experiments were carried out in Randomized Complete Blocks in the fall-winter and spring-summer planting periods. To compare the three selection methods, usually employed in population breeding genetics the expected genetic gains were estimated considering each blockor plot as strata, and mass selection between and within the half-sib progenies. Samples of 15 marketable roots per plot were evaluated at the individual level for the characters root length (RL) and root shape index (SI). A joint analysis of variance, weighted for the differences in number of replications between the experiments was performed for the six common traits. The results of the genetic parameter estimates of the single variance analysis indicated that the variety Campinas was best adapted to the fall-winter planting period. Heritabilities greater than 60 per cent were observed for the majority of traits assessed at the plot level. The selecction against the trait premature flowering (PF) may result in satisfactory genetic gain in the two environmental conditions because of the high genetic variability coefficients obtained. The percentage of marketable cylindrical roots (MCR) demonstrated an expected genetic gain per cycle of only 4.82 per cent in the fall-winter period, probably because it had already been selected, for various cycles, under these environmental conditions. On the other hand, in the spring-suminer planting period, the genetic gain was estimated to be 14.44 per cent. Total and marketable yields were high in the fall-winter period and low in the spring-summer period. For the traits RL and SI, assessed at the individual level, the stratified mass selection, considering each plot as strata, was less efficient in relation to the other proposed selection methods. Therefore it is concluded that breeding of the variety Caampinas, based on the performance of the half-sib progenies for root quality and yield is fairly promising within each planting period, but simultaneous selection for both periods is difficult.