Carrot vernalization requirement (VR), the amount of cold exposure needed for plants to become vernalized, strongly influences geographical adaptation of the crop and many agricultural practices, and this trait defines annual vs. biennial cultivars. Despite its importance, the genetic and molecular mechanisms governing carrot VR remain elusive. Here, we integrated inheritance, linkage mapping, genome wide association studies (GWAS), phylogenetic analysis, and transcriptomics of coding and noncoding mRNA data to dissect the genetic control of carrot VR. A simply-inherited dominant locus controlling VR, denominated Vrn1, was identified and genetically mapped at the distal end of chromosome 2, in a highly-saturated genotyping-by-sequencing (GBS)-derived linkage map. GWAS results revealed a 694 kb region with strong marker-trait associations that overlapped Vrn1. In this region, we identified two duplicated SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1) genes, termed DcSOC1-1 and DcSOC1-2, that were phylogenetically related to SOC1 genes from other species, and were strongly upregulated in vernalized plants relative to non-vernalized plants of annual and biennial carrots. Further, the identification and transcriptome analysis of carrot homologs to Arabidopsis vernalization and flowering genes revealed additional key genes from these pathways exhibiting correlated expression profiles with DcSOC1-1 and DcSOC1-2, including other SOC1, FUL (FRUITFUL) and FLC (FLOWERING LOCUS C) genes. The expression profiles of DcSOC1-1, DcSOC1-2, and five other vernalization-related genes were validated by RT-qPCR analysis. No differentially expressed ncRNAs directly related to the Vrn1 candidates were identified. Overall, this study provides strong linkage-mapping and functional evidences for the candidacy of DcSOC1-1 and DcSOC1-2 as the primary regulators of VR in carrot.

Phelipanche aegyptiaca is a root parasitic plant that causes significant yield losses in many crops, including carrots (Daucus carota). This study investigates the resistance mechanisms of two wild carrot accessions, PI 21793 (Daucus glaber) and PI 341902 (Daucus littoralis), against P. aegyptiaca compared to a cultivated carrot (P0114; D. carota). Wild carrots induced lower germination rates of P. aegyptiaca seeds and fewer successful tubercles, indicating both pre-attachment and partial post-attachment resistance mechanisms. Strigolactone analysis revealed significant quantitative differences between cultivated and wild carrots. While cultivated carrots exuded high levels of two strigolactones, one of which was putatively identified as the non-canonical strigolactone, 4-oxo-methyl-carlalactone, wild carrots released lower amounts of these compounds. Supplementation with the artificial strigolactone analog GR24 increased germination in P. aegyptiaca inoculated on wild carrots, suggesting that strigolactone deficiency and possibly altered composition are key pre-attachment resistance mechanisms. However, higher germination resulted in no significant improvement in tubercle development on wild carrots. Parasite seedlings showed necrosis-like symptoms at their attachment sites on wild carrot roots, indicating an additional post-attachment resistance mechanism. These findings provide new insights into strigolactone-mediated host resistance and highlight the potential of wild carrot accessions to contribute to the development of resistant cultivars against parasitic plants.

In this study, 36 carrot breeding lines and cultivars widely used for organic production were grown for 4 years in two locations under organic and conventionally managed trials. Highly significant genotypic main effects and genotype × year and, to a lesser extent, genotype × location interactions were observed for all traits, including harvest root and top weight as well as top height and width measured at early season, midseason, and the time of harvest. In contrast, management systems and most management system interactions were not significant. Broad sense heritability (repeatability) for most responses was relatively high (≥0.75), suggesting a high potential for genetic gains through selection, although early-season top height and width heritability were somewhat lower. High rank correlations were found for all traits when comparing genotypes grown under organic and conventional management in both locations when evaluated across all years for each location (P ≤ 0.001) or with few exceptions when evaluated by individual years (P ≤ 0.05). An analysis of F1 hybrid cultivars and comparison of the performance of production systems showed no rank correlations for most traits and years. In contrast to the results observed for F1 hybrid cultivars, open-pollinated breeding lines presented more instances of correlation between management systems in given locations and years. The stability analysis provided insights into the relative stability or adaptability of 36 carrot genotypes (cultivars) across environments. Considering all traits evaluated, several open-pollinated and hybrid cultivars demonstrated consistent performance along the environmental index, whereas other cultivars and the more inbred breeding lines did not. An additive main effects and multiplicative interactions analysis did not present any clear patterns for management system or location, but it did reflect the highly significant effect of year in genotype × environment interactions. The first and second principal components explain a range of total variance from 41.8% for early top height to 55.2% for harvest top weight. The results of the current study contribute to the body of knowledge regarding genotype X management system interactions and provide insights into implications for organic crop improvement in carrot. The results further aid in understanding the influence of organic management in horticultural crops, which may differ with the results of grain crops.

Carrot (Daucus carota L.) is a globally cultivated root vegetable with significant genetic diversity. This first study generated and validated carrot InDels to unravel the genetic divergence between Eastern and Western gene pools, integrating agro-morphometric traits with functional InDel markers. Eastern accessions exhibited larger plants, bigger roots with diverse colors, while Western accessions were more uniform orange color and compact in architecture. From RNA-seq data, 271 agarose-resolvable functional InDels (>15bp length difference) were identified, of which 48 validated markers showed high polymorphism (84.21%) across two gene pools supporting secondary domestication changes. Located in coding and UTR regions, these InDels likely regulate gene expression and may have contributed to significant genetic modifications among carrot gene pools. Genetic diversity in the Western gene pool indicated more intense selection and domestication. Population structure and phylogenetic analysis revealed clear gene pool differentiation (Fst = 0.181) with potential gene flow (Nm = 1.716). Functional annotation of linked InDels to key biological processes, highlighted their role in domestication. Key InDels (DcFInDel32, DcFInDel28, and DcFInDel55) were associated with multiple traits, underscoring their utility in marker-assisted selection (MAS). These findings provide insights for developing improved carrot cultivars with high yield and quality adapted to diverse climates.

Abstract Carrots (Daucus carota L.) are a rich source of provitamin A, namely, α‐ and β‐carotene. Breeding programs prioritize increasing β‐carotene content for improved color and nutrition. Understanding the genetic basis of carotenoid accumulation is crucial for implementing genomic‐assisted selection to develop high‐carotenoid lines. While previous studies identified loci (Y2, Y, Or, and REC) associated with carrot color and carotenoid content, this study employed genome‐wide association (GWA) in a diverse panel of 738 carrot accessions. We discovered a novel locus with a candidate gene encoding phytoene synthase, a key enzyme in carotenoid biosynthesis. The Y2, Y, Or, and REC loci are mostly fixed in orange varieties, yet considerable variation in carotenoid concentration persists. This suggests a multigenic trait influenced by the environment. GWA of carotenoid concentration identified a quantitative trait locus for total carotenoids and α‐carotene. We explored the accuracy of genomic prediction (GP) models to predict carotenoid concentration. We determined the optimal number of plants and plots required for accurate carotenoid phenotyping, finding ≥5 plants per plot and three plots per site as the minimum effective sample per accession. GP models achieved accuracies ranging from 0.06 to 0.40 depending on the carotenoid measured and environment the carrots were assayed. Additional studies in breeding programs will clarify the potential of genomic‐assisted selection for high‐carotenoid carrots.

Biennial vegetable crops are challenging to breed due to long breeding cycle times. At the same time, it is important to preserve a strong biennial growth habit, avoiding premature flowering that renders the crop unmarketable. Gene banks carry important genetic variation which may be essential to improve crop resilience, but these collections are underutilized due to lack of characterization for key traits like bolting tendency for biennial vegetable crops. Due to concerns about introducing undesirable traits such as premature flowering into elite germplasm, many accessions may not be considered for other key traits that benefit growers, leaving crops more vulnerable to pests, diseases, and abiotic stresses. In this study, we develop a method for characterizing flowering to identify accessions that are predominantly biennial, which could be incorporated into biennial breeding programs without substantially increasing the risk of annual growth habits. This should increase the use of these accessions if they are also sources of other important traits such as disease resistance. We developed the CarrotOmics flowering habit trait ontology and evaluated flowering habit in the largest (N=695), and most diverse collection of cultivated carrots studied to date. Over 80% of accessions were collected from the Eurasian supercontinent, which includes the primary and secondary centers of carrot diversity. We successfully identified untapped genetic diversity in biennial carrot germplasm (n=197 with 0% plants flowering) and predominantly-biennial germplasm (n=357 with <15% plants flowering). High broad-sense heritability for flowering habit (0.81 < H2< 0.93) indicates a strong genetic component of this trait, suggesting that these carrot accessions should be consistently biennial. Breeders can select biennial plants and eliminate annual plants from a predominantly biennial population. The establishment of the predominantly biennial subcategory nearly doubles the availability of germplasm with commercial potential and accounts for 54% of the germplasm collection we evaluated. This subcollection is a useful source of genetic diversity for breeders. This method could also be applied to other biennial vegetable genetic resources and to introduce higher levels of genetic diversity into commercial cultivars, to reduce crop genetic vulnerability. We encourage breeders and researchers of biennial crops to optimize this strategy for their particular crop.

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites more strongly associated with fungal than bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

Carrot (Daucus carota L.) is a nutrient-rich vegetable that is widely cultivated and consumed in Pakistan in both raw and processed form. Data on the proximate composition and natural occurrence of aflatoxins (AFs) in carrots and marketed carrot products is lacking in Pakistan and the risk exposure of AF has not been characterised before. Thus, the current study was designed to know the frequently consumed carrot products with per capita consumption, and risk assessment of AF through these products in various regions of South Punjab Pakistan. A survey was conducted with 125 respondents and appeared that raw carrot, fresh carrot juice, gajrella and pickle are the most frequently consumed marketed carrot products with per capita consumption i.e. 62.5, 46.6, 16.2 and 14.5 gday-1, respectively. Proximate analysis revealed that carrot root and processed carrot products contained 9.65-98.2% moisture, 0.23-0.60% ash, 6.2-14.1% carbohydrates, 0.31-0.80% protein, 0.40-3.7% fat and 1.4-4.20% fibre. AF analysis revealed that 36.67% of samples were contaminated with TAF. Thirty-five (35%) percent of samples were tainted with aflatoxin B1, and 13.33% of samples were contaminated with aflatoxin B2. All the samples of carrot root, fresh carrot juice and gajrella contained TAF levels less than the maximum limit (ML) (2 ppb) assigned by the European Union (EU). However, the entire AFB1 positive samples of carrot pickle contained AFB1 levels of more than 2 ppb exceeding the ML. Furthermore, daily dietary exposure of TAFs ranged from 0.11 to 1.27 ng/kg of body weight per day which relatively exceeds the permissible limit of 1 ng/kg of body weight per day as defined by the Joint FAO/WHO Expert Committee on Food Additives. This is the first prevalence and risk assessment report of AF in marketed processed carrot products in Pakistan. These baseline data are an initial step in the effort to deal with this significant food safety issue and the establishment of legislation for AF in marketed products is needed in Pakistan.

Background/Objectives: Carrot is a major root vegetable in the Apiaceae owing to its abundant carotenoids, antioxidants, vitamins, and minerals. The modern dark orange western carrot was derived from sequential domestication events from the white-rooted wild form to the pale orange-, purple-, or yellow-rooted eastern carrot. Genetic and molecular studies between eastern and western carrots are meager despite their evolutionary relatedness. Methods: Twelve RNA seq libraries obtained from distinct eastern and western cultivars at vegetative and reproductive developmental stages were utilized to identify differentially expressed genes (DEGs) to decode the key molecular genetic changes in carotenoid and flowering pathways. Results: In the carotenoid pathway, an upregulation of the PSY, CRTISO, and LCYE genes was observed in the western cultivar, while the eastern cultivar exhibited a higher abundance of downstream enzymes, particularly CCD and NCED1. These later enzymes are crucial in linking apocarotenoids and xanthin-mediated ABA signaling. In the flowering pathway, we noted a greater expression of DEGs associated with the photoperiod and vernalization pathways in the western cultivar. In contrast, the eastern cultivar displayed a dominance of genes from the autonomous pathway (FLD, LD, FLK, and PEBP) that function to repress FLC. The experimental validation of 12 key genes through quantitative real-time PCR further confirms their functional role in carrots. Conclusions: The identified key regulatory genes in these major pathways are valuable for designing breeding strategies for manipulating carotenoid content and flowering time while developing climate-specific carrots. The knowledge of carotenoid and flowering pathways is advantageous in producing nutritionally improved roots and seeds in carrots across diverse climates.

Carrot (Daucus carota L.) is a high value, nutritious, and colorful crop, but delivering carrots from seed to table can be a struggle for carrot growers. Weed competitive ability is a critical trait for crop success that carrot and its apiaceous relatives often lack owing to their characteristic slow shoot growth and erratic seedling emergence, even among genetically uniform lines. This study is the first field-based, multi-year experiment to evaluate shoot-growth trait variation over a 100-day growing season in a carrot diversity panel (N=695) that includes genetically diverse carrot accessions from the United States Department of Agriculture National Plant Germplasm System. We report phenotypic variability for shoot-growth characteristics, the first broad-sense heritability estimates for seedling emergence (0.68 < H2 < 0.80) and early-season canopy coverage ( 0.61 < H2 < 0.65), and consistent broad-sense heritability for late-season canopy height (0.76 < H2 < 0.82), indicating quantitative inheritance and potential for improvement through plant breeding. Strong correlation between emergence and canopy coverage (0.62 < r < 0.72) suggests that improvement of seedling emergence has great potential to increase yield and weed competitive ability. Accessions with high emergence and vigorous canopy growth are of immediate use to breeders targeting stand establishment, weed-tolerance, or weed-suppressant carrots, which is of particular advantage to the organic carrot production sector, reducing the costs and labor associated with herbicide application and weeding. We developed a standardized vocabulary and protocol to describe shoot-growth and facilitate collaboration and communication across carrot research groups. Our study facilitates identification and utilization of carrot genetic resources, conservation of agrobiodiversity, and development of breeding stocks for weed-competitive ability, with the long-term goal of delivering improved carrot cultivars to breeders, growers, and consumers. Accession selection can be further optimized for efficient breeding by combining shoot growth data with phenological data in this study’s companion paper to identify ideotypes based on global market needs.

Carrot is an important root vegetable and salinity has strong effect on its seed germination and seedling characters. An experiment was conducted at the Postgraduate Laboratory of the Department of Horticulture, Bangladesh Agricultural University, Mymensingh during the period from July to August, 2023 to study the effect of salinity stress on the seed germination and seedling characters of four carrot varieties. The two-factor experiment consisted of four carrot varieties viz. Orange king, Orange star, Sangal and Red lady, and five salinity levels viz. control (tap water), 25 mM, 50 mM, 75 mM and 100 mM NaCl. The experiment was laid out in completely randomized design with three replications. Results revealed that salinity and carrot varieties significantly influenced all the parameters studied. The highest seed germination (44.44%) was obtained from Orange king while the lowest (32.89%) was obtained from Red lady. The highest seed germination (41.11%) was obtained from 100 mM NaCl solution and the lowest (34.44%) was found from 75 mM NaCl. Among the treatment combinations, the highest seed germination (60.00%) was obtained from Orange king along with 50 mM NaCl. The maximum radicle (15.46 mm) and plumule length (12.36 mm), leaf size (5.50 mm), number of leaves (2.73) and seedling height (27.82 mm) was obtained from Orange king. Maximum plumule length (13.27 mm), leaf size (5.98 mm) and seedling height (23.27mm) was obtained from control treatment and maximum number of leaves (2.08) from 25 mM NaCl solution. Among the treatment combinations, highest radicle length (18.27 mm), plumule length (17.40 mm), leaf size (7.60 mm), seedling height (35.67 mm) was obtained from Orange king along with 25 mM NaCl solution. Therefore, Orange king along with 50 mM NaCl solution and 25 mM NaCl solution was found to be better in respect of seed germination and seedling characters of carrots compared to other treatments respectively.

Drought is one of the major environmental challenges constraining the production of agricultural crops, including carrot. Seed germination is the initial and most critical stage of crop establishment, and it is very sensitive to drought stress because water scarcity affects the enzymatic solubilization of stored metabolites in seeds that provide energy for the growth of germinating embryo. Few studies evaluating the effect of drought stress on carrot seed germination of more than a few cultivars grown under stress have been published. Therefore, the present study was designed to define the appropriate osmotic potential for evaluating drought tolerance of carrot, evaluate the response of diverse carrot germplasm to drought stress during seed germination to identify drought-tolerant accessions that may be used by plant breeders, and evaluate the relation between amylase activity and germination rate of drought-tolerant and drought-sensitive accessions. To identify an appropriate screening osmotic potential, two commercial cultivars and two United States Department of Agriculture inbreeds were evaluated at six osmotic potentials (00, −0.30, −0.51, −0.58, −0.80, and −1.05 MPa); −0.58 MPa was identified as the optimal osmotic potential for screening the drought tolerance of carrot seed. Cultivated and wild carrot plant introductions (PIs) (n = 200 and n = 50, respectively) from the National Plant Germplasm System were evaluated for drought tolerance under nonstress and simulated drought stress conditions (00 MPa and −0.58 MPa, respectively) by calculating the absolute decrease (AD) in percent germination, inhibition index (II), relative drought tolerance (RDT), and drought tolerance index (DTI). All measurements of drought tolerance identified significant differences among accessions; the AD in seed germination ranged from 0.0% to 69.3%, II ranged from 0.0% to 80.2%, RDT ranged from 0.2 to 1.0, and DTI ranged from 0.13 to 1.47. All wild carrot accessions displayed low levels of drought tolerance, but PI 652387 and PI 177381 (both from Turkey) and PI 274297 (Pakistan) were most drought-sensitive, whereas cultivated accessions PI 643114 (United States), PI 652208 (China), and PI 502347 (Uzbekistan) were most drought-tolerant. Tolerant accessions displayed much higher α-amylase activity under nonstress conditions than sensitive accessions, and α-amylase activity of tolerant accessions was also reduced less with seed germination under increasing osmotic potential (range, 0.0 to −1.05 MPa) than sensitive accessions over 24, 48, and 72 hours of seed germination. This is the first evaluation of drought stress tolerance during seed germination and the enzymatic response of diverse carrot germplasms under simulated drought stress.