Evaluation of shoot-growth variation in diverse carrot (Daucus carota L.) germplasm for genetic improvement of stand establishment.

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.

Advancing utilization of diverse global carrot (Daucus carota L.) germplasm with flowering habit trait ontology.

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.

Proximate composition and prevalence and exposure assessment of aflatoxins intake through consumption of fresh carrot and processed marketed carrot products in South Punjab, Pakistan.

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.

Characterization of Purple Carrot Germplasm for Antioxidant Capacity and Root Concentration of Anthocyanins, Phenolics, and Carotenoids.

The present study characterized a genetically and phenotypically diverse collection of 27 purple and two non-purple (one orange and one yellow) carrot accessions for concentration of root anthocyanins, phenolics, and carotenoids, and antioxidant capacity estimated by four different methods (ORAC, DPPH, ABTS, FRAP), in a partially replicated experimental design comprising data from two growing seasons (2018 and 2019). Broad and significant (p < 0.0001) variation was found among the accessions for all the traits. Acylated anthocyanins (AA) predominated over non-acylated anthocyanins (NAA) in all the accessions and years analyzed, with AA accounting for 55.5-100% of the total anthocyanin content (TAC). Anthocyanins acylated with ferulic acid and coumaric acid were the most abundant carrot anthocyanins. In general, black or solid purple carrots had the greatest TAC and total phenolic content (TPC), and the strongest antioxidant capacities, measured by all methods. Antioxidant capacity, estimated by all methods, was significantly, positively, and moderately-to-strongly correlated with the content of all individual anthocyanins pigments, TAC, and TPC, in both years (r = 0.59-0.90, p < 0.0001), but not with the carotenoid pigments lutein and ß-carotene; suggesting that anthocyanins and other phenolics, but not carotenoids, are major contributors of the antioxidant capacity in purple carrots. We identified accessions with high concentration of chemically stable AA, with potential value for the production of food dyes, and accessions with relatively high content of bioavailable NAA that can be selected for increased nutraceutical value (e.g., for fresh consumption).

Anthocyanin and Lycopene Contents Do Not Affect ß-Carotene Bioefficacy from Multicolored Carrots (Daucus carota L.) in Male Mongolian Gerbils.

BACKGROUND: Anthocyanins and carotenoids are phytochemicals that may benefit health through provitamin A carotenoid (PAC), antioxidant, and anti-inflammatory activities. These bioactives may mitigate chronic diseases. Consumption of multiple phytochemicals may impact bioactivity in synergistic or antagonistic manners. OBJECTIVES: Two studies in weanling male Mongolian gerbils assessed the relative bioefficacy of ß-carotene equivalents (BCEs) to vitamin A (VA) with simultaneous consumption of the non-PAC lycopene or anthocyanins from multicolored carrots. METHODS: After 3-wk VA depletion, 5-6 gerbils were killed as baseline groups. The remaining gerbils were divided into 4 carrot treatment groups; the positive control group received retinyl acetate and the negative control group was given vehicle soybean oil (n = 10/group; n = 60/study). In the lycopene study, gerbils consumed feed varying in lycopene sourced from red carrots. In the anthocyanin study, gerbils consumed feed varying in anthocyanin content sourced from purple-red carrots, and positive controls received lycopene. Treatment feeds had equalized BCEs: 5.59 ± 0.96 µg/g (lycopene study) and 7.02 ± 0.39 µg/g (anthocyanin study). Controls consumed feeds without pigments. Serum, liver, and lung samples were analyzed for retinol and carotenoid concentrations using HPLC. Data were analyzed by ANOVA and Tukey's studentized range test. RESULTS: In the lycopene study, liver VA did not differ between groups (0.11 ± 0.07 µmol/g) indicating no effect of varying lycopene content. In the anthocyanin study, liver VA concentrations in the medium-to-high (0.22 ± 0.14 µmol/g) and medium-to-low anthocyanin (0.25 ± 0.07 µmol/g) groups were higher than the negative control (0.11 ± 0.07 µmol/g) (P < 0.05). All treatment groups maintained baseline VA concentrations (0.23 ± 0.06 µmol/g). Combining studies, serum retinol had 12% sensitivity to predict VA deficiency, defined as 0.7 µmol/L. CONCLUSIONS: These gerbil studies suggested that simultaneous consumption of carotenoids and anthocyanins does not impact relative BCE bioefficacy. Breeding carrots for enhanced pigments to improve dietary intake should continue.

CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota).

CarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601 Apiales species (or subspecies) and descriptions of 9408 accessions from 11 germplasm collections representing more than 600 of these species. Additionally, 204 Apiales species have phenotypic information, totaling 28 517 observations from 10 041 biological samples. Resources on CarrotOmics are freely available, search functions are provided to find data of interest and video tutorials are available to describe the search functions and genomic tools. CarrotOmics is a timely resource for the Apiaceae research community and for carrot geneticists developing improved cultivars with novel traits addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables and a dynamic environment due to climate change. Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency. DATABASE URL: https://carrotomics.org/.

Physicochemical properties, degradation kinetics, and antioxidant capacity of aqueous anthocyanin-based extracts from purple carrots compared to synthetic and natural food colorants.

As a means to evaluate the potential of carrot anthocyanins as food colorants and nutraceutical agents, we investigated the physicochemical stability and antioxidant capacity of purple carrot extracts under different pH (2.5-7.0) and temperature (4-40 °C) conditions, in comparison to a commercial synthetic (E131) and a natural grape-based (GRP) colorant. During incubation, the colorants were weekly-monitored for various color parameters, concentration of anthocyanins and phenolics, and antioxidant capacity. Carrot colorants were more stable than GRP; and their thermal stability was equal (at 4 °C) or higher than that of E131 (at 25-40 °C). Carrot anthocyanins had lower degradation rate at low pH and temperature, with acylated anthocyanins (AA) being significantly more stable than non-acylated anthocyanins (NAA). Anthocyanins acylated with feruloyl and coumaroyl glycosides were the most stable carrot pigments. The higher stability of carrot colorants is likely due to their richness in AA and -to a lesser extent- copigmentation with other phenolics.

Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values.

KEY MESSAGE: The principal phenotypic determinants of market class in carrot-the size and shape of the root-are under primarily additive, but also highly polygenic, genetic control. The size and shape of carrot roots are the primary determinants not only of yield, but also market class. These quantitative phenotypes have historically been challenging to objectively evaluate, and thus subjective visual assessment of market class remains the primary method by which selection for these traits is performed. However, advancements in digital image analysis have recently made possible the high-throughput quantification of size and shape attributes. It is therefore now feasible to utilize modern methods of genetic analysis to investigate the genetic control of root morphology. To this end, this study utilized both genome wide association analysis (GWAS) and genomic-estimated breeding values (GEBVs) and demonstrated that the components of market class are highly polygenic traits, likely under the influence of many small effect QTL. Relatively large proportions of additive genetic variance for many of the component phenotypes support high predictive ability of GEBVs; average prediction ability across underlying market class traits was 0.67. GWAS identified multiple QTL for four of the phenotypes which compose market class: length, aspect ratio, maximum width, and root fill, a previously uncharacterized trait which represents the size-independent portion of carrot root shape. By combining digital image analysis with GWAS and GEBVs, this study represents a novel advance in our understanding of the genetic control of market class in carrot. The immediate practical utility and viability of genomic selection for carrot market class is also described, and concrete guidelines for the design of training populations are provided.

Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem.

In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of 'root outer phloem anthocyanin pigmentation' (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.

Development of Carrot Nutraceutical Products as an Alternative Supplement for the Prevention of Nutritional Diseases.

Nutraceuticals can serve as an alternative supplement to overcome nutritional deficiency for a healthy lifestyle. They can also play a key role in disease management. To develop carrot nutraceutical products, 64 genotypes from four different continents were evaluated for a range of morpho-nutrition variables. Genetic variability, heritability, strength and direction of association among variables, and direct and indirect relationships among physiochemical and nutritional traits with ß-carotene content were evaluated. Core diameter, foliage weight, root weight and shoulder weight showed significant association with ß-carotene accumulation. Principal component analysis for physiochemical and nutritional assessment divided these genotypes into two distinctive groups, Eastern carrots and Western carrots. Caloric and moisture content had high positive associations with ß-carotene content while carbohydrate content was negatively associated. Five genotypes (T-29, PI 634658, PI 288765, PI 164798, and Ames 25043) with the highest ß-carotene contents were selected for making three nutraceutical supplements (carrot-orange juice, carrot jam and carrot candies). These nutraceutical supplements retained high ß-carotene content coupled with antioxidant properties. Carrot jam (6.5 mg/100 g) and carrot candies (4.8 mg/100 g) had greater concentrations of ß-carotene than carrot-orange juice (1.017 mg/100 g). Carrot jam presented high antioxidant activity with the highest values in T-29 (39% inhibition of oxidation) followed by PI 634658 (37%), PI 164798 (36.5%), Ames 25043 (36%) and PI 288765 (35.5%). These nutraceutical products, with 4-6.5 mg/100 g ß-carotene content, had higher values than the USDA recommended dietary intake of 3-6 mg ß-carotene/day can be recommended for daily use to lower the risk of chronic disease.

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root.

BACKGROUND: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. METHODS: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. RESULTS: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. CONCLUSIONS: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root.

Overlapping Vitamin A Interventions with Provitamin A Carotenoids and Preformed Vitamin A Cause Excessive Liver Retinol Stores in Male Mongolian Gerbils.

BACKGROUND: Vitamin A (VA) deficiency is a public health problem in some countries. Fortification, supplementation, and increased provitamin A consumption through biofortification are efficacious, but monitoring is needed due to risk of excessive VA intake when interventions overlap. OBJECTIVES: Two studies in 28-36-d-old male Mongolian gerbils simulated exposure to multiple VA interventions to determine the effects of provitamin A carotenoid consumption from biofortified maize and carrots and preformed VA fortificant on status. METHODS: Study 1 was a 2 × 2 × 2 factorial design (n = 85) with high-ß-carotene maize, orange carrots, and VA fortification at 50% estimated gerbil needs, compared with white maize and white carrot controls. Study 2 was a 2 × 3 factorial design (n = 66) evaluating orange carrot and VA consumption through fortification at 100% and 200% estimated needs. Both studies utilized 2-wk VA depletion, baseline evaluation, 9-wk treatments, and liver VA stores by HPLC. Intestinal scavenger receptor class B member 1 (Scarb1), ß-carotene 15,15'-dioxygenase (Bco1), ß-carotene 9',10'-oxygenase (Bco2), intestine-specific homeobox (Isx), and cytochrome P450 26A1 isoform α1 (Cyp26a1) expression was analyzed by qRT-PCR in study 2. RESULTS: In study 1, liver VA concentrations were significantly higher in orange carrot (0.69 ± 0.12 µmol/g) and orange maize groups (0.52 ± 0.21 µmol/g) compared with baseline (0.23 ± 0.069 µmol/g) and controls. Liver VA concentrations from VA fortificant alone (0.11 ± 0.053 µmol/g) did not differ from negative control. In study 2, orange carrot significantly enhanced liver VA concentrations (0.85 ± 0.24 µmol/g) relative to baseline (0.43 ± 0.14 µmol/g), but VA fortificant alone (0.42 ± 0.21 µmol/g) did not. Intestinal Scarb1 and Bco1 were negatively correlated with increasing liver VA concentrations (P < 0.01, r2 = 0.25-0.27). Serum retinol concentrations did not differ. CONCLUSIONS: Biofortified carrots and maize without fortification prevented VA deficiency in gerbils. During adequate provitamin A dietary intake, preformed VA intake resulted in excessive liver stores in gerbils, despite downregulation of carotenoid absorption and cleavage gene expression.

Carrot Leaves Maintain Liver Vitamin A Concentrations in Male Mongolian Gerbils Regardless of the Ratio of α- to ß-Carotene When ß-Carotene Equivalents Are Equalized.

BACKGROUND: Carrots are an important horticultural crop that contain provitamin A carotenoids (PACs). Orange carrots have high concentrations of α-carotene, which upon central cleavage yields 1 retinal and 1 α-retinal molecule. The leaves of carrot plants are a source of PACs when consumed. OBJECTIVE: Male Mongolian gerbils aged 27-30 d were used to assess the bioefficacy of carrot leaves to maintain vitamin A (VA) status and investigate whether the ratio of α- to ß-carotene (α:ß-carotene) affected bioefficacy. METHODS: After 3 wk depletion, baseline gerbils were killed (n = 6) and the remaining gerbils (n = 60) were divided into 6 groups to receive 4 VA-deficient, carrot leaf-fortified feeds (1:1.4, 1:2.5, 1:5.0, and 1:80 α:ß-carotene ratio) equalized to 4.8 nmol/g ß-carotene equivalents (ßCEs), or VA-deficient feed with (VA+) or without (VA-) retinyl acetate supplements. Carrot-leaf powder from 4 carrot plants with differing α:ß-carotene ratios was used. After 4 wk, gerbils were killed and tissues were collected and analyzed for retinoids by HPLC. RESULTS: VA+ had higher total liver VA (means ± SD 0.91 ± 0.29 µmol) than all other groups (range: 0.40-0.62) (P ≤ 0.03), and the carrot leaf treatments did not differ from baseline (0.55 ± 0.09 µmol). VA- (0.40 ± 0.23 µmol VA/liver) did not differ from the leaf-fed groups, but 30% became VA deficient (defined as <0.1 µmol VA/g liver). α-Retinol accumulated in livers and lungs and was correlated to total α-carotene consumption (R2 = 0.83 and 0.88, respectively; P < 0.0001). Bioefficacy factors ranged from 4.2 to 6.2 µg ßCE to 1 µg retinol. CONCLUSIONS: Carrot leaves maintain VA status and prevent deficiency in gerbils regardless of the α:ß-carotene ratio. The bioconversion of PACs from carrot leaves to retinol is similar to what has been reported for other green leafy vegetables, making the consumption of carrot leaves a viable method to improve dietary PAC intake.

Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.).

KEY MESSAGE: Inheritance, QTL mapping, phylogenetic, and transcriptome (RNA-Seq) analyses provide insight into the genetic control underlying carrot root and leaf tissue-specific anthocyanin pigmentation and identify candidate genes for root phloem pigmentation. Purple carrots can accumulate large quantities of anthocyanins in their root tissues, as well as in other plant parts. This work investigated the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root phloem and xylem, and in leaf petioles. Inheritance of anthocyanin pigmentation in these three tissues was first studied in segregating F2 and F4 populations, followed by QTL mapping of phloem and xylem anthocyanin pigments (independently) onto two genotyping by sequencing-based linkage maps, to reveal two regions in chromosome 3, namely P1 and P3, controlling pigmentation in these three tissues. Both P1 and P3 condition pigmentation in the phloem, with P3 also conditioning pigmentation in the xylem and petioles. By means of linkage mapping, phylogenetic analysis, and comparative transcriptome (RNA-Seq) analysis among carrot roots with differing purple pigmentation phenotypes, we identified candidate genes conditioning pigmentation in the phloem, the main tissue influencing total anthocyanin levels in the root. Among them, a MYB transcription factor, DcMYB7, and two cytochrome CYP450 genes with putative flavone synthase activity were identified as candidates regulating both the presence/absence of pigmentation and the concentration of anthocyanins in the root phloem. Concomitant expression patterns of DcMYB7 and eight anthocyanin structural genes were found, suggesting that DcMYB7 regulates transcription levels in the latter. Another MYB, DcMYB6, was upregulated in specific purple-rooted samples, suggesting a genotype-specific regulatory activity for this gene. These data contribute to the understanding of anthocyanin regulation in the carrot root at a tissue-specific level and maybe instrumental for improving carrot nutritional value.

Total Adipose Retinol Concentrations Are Correlated with Total Liver Retinol Concentrations in Male Mongolian Gerbils, but Only Partially Explained by Chylomicron Deposition Assessed with Total α-Retinol.

BACKGROUND: Liver vitamin A (VA) concentration is the gold standard for VA status, but is not routinely accessible. Adipose tissue VA concentrations, as retinol and retinyl esters, may be correlated to liver VA. α-VA (as α-retinol) is a cleavage product of α-carotene that traces postprandial VA distribution to tissues but cannot recirculate from hepatic stores, providing insight into tissue VA sources. OBJECTIVE: We performed a secondary analysis of VA and α-VA in Mongolian gerbil liver and adipose to determine the suitability of adipose tissue VA as a biomarker of VA status. METHODS: Gerbils (n = 186) consumed feeds containing 0-15.9 µg (0-55.6 nmol) retinol activity equivalents/g as preformed VA and/or provitamin A carotenoids for 36-62 d in 3 studies. Body fat percentage was determined in the final study by MRI. Serum and liver retinol, α-retinol, and retinyl esters were extracted and analyzed by HPLC or ultra-performance LC (UPLC). Epididymal and retroperitoneal adipose tissue retinol and α-retinol were determined by UPLC after homogenization, saponification, and extraction. Linear regression models with appropriate data transformations identified determinants of adipose VA concentrations. RESULTS: Liver VA did not predict serum retinol concentrations. After logarithmic transformation of adipose and liver values, liver VA positively predicted both adipose depots' VA concentrations (P < 0.001, R 2 > 0.7). Adding serum retinol or body fat percentage did not significantly increase the adjusted R 2. In liver, α-VA concentration explained much of the variation of VA (P < 0.001, R 2 > 0.7), but far less in epididymal and retroperitoneal adipose (P = 0.004 and 0.012, respectively, R 2 < 0.4). CONCLUSIONS: Adipose VA is correlated with liver VA and is a potential biomarker of VA status. It is not fully explained by chylomicron deposition and is negatively affected by serum retinol. Adipose biopsy validation is needed for human applications.

Identification of an SCPL Gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root.

Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made toward understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root.

An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot (Daucus carota L.).

Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.

Carotenoid Presence Is Associated with the Or Gene in Domesticated Carrot.

Carrots are among the richest sources of provitamin A carotenes in the human diet, but genetic variation in the carotenoid pathway does not fully explain the high levels of carotenoids in carrot roots. Using a diverse collection of modern and historic domesticated varieties, and wild carrot accessions, an association analysis for orange pigmentation revealed a significant genomic region that contains the Or gene, advancing it as a candidate for carotenoid presence in carrot. Analysis of sequence variation at the Or locus revealed a nonsynonymous mutation cosegregating with carotenoid content. This mutation was absent in all wild carrot samples and nearly fixed in all orange domesticated samples. Or has been found to control carotenoid presence in other crops but has not previously been described in carrot. Our analysis also allowed us to more completely characterize the genetic structure of carrot, showing that the Western domesticated carrot largely forms one genetic group, despite dramatic phenotypic differences among market classes. Eastern domesticated and wild accessions form a second group, which reflects the recent cultivation history of carrots in Central Asia. Other wild accessions form distinct geographic groups, particularly on the Iberian peninsula and in Northern Africa. Using genome-wide Fst , nucleotide diversity, and the cross-population composite likelihood ratio, we analyzed the genome for regions putatively under selection during domestication and identified 12 regions that were significant for all three methods of detection, one of which includes the Or gene. The Or domestication allele appears to have been selected after the initial domestication of yellow carrots in the East, near the proposed center of domestication in Central Asia. The rapid fixation of the Or domestication allele in almost all orange and nonorange carrots in the West may explain why it has not been found with less genetically diverse mapping populations.

Dissecting the Genetic Architecture of Shoot Growth in Carrot (Daucus carota L.) Using a Diallel Mating Design.

Crop establishment in carrot (Daucus carota L.) is limited by slow seedling growth and delayed canopy closure, resulting in high management costs for weed control. Varieties with improved growth habit (i.e., larger canopy and increased shoot biomass) may help mitigate weed control, but the underlying genetics of these traits in carrot is unknown. This project used a diallel mating design coupled with recent Bayesian analytical methods to determine the genetic basis of carrot shoot growth. Six diverse carrot inbred lines with variable shoot size were crossed in WI in 2014. F1 hybrids, reciprocal crosses, and parental selfs were grown in a randomized complete block design with two blocks in WI (2015) and CA (2015, 2016). Measurements included canopy height, canopy width, shoot biomass, and root biomass. General and specific combining abilities were estimated using Griffing's Model I, which is a common analysis for plant breeding experiments. In parallel, additive, inbred, cross-specific, and maternal effects were estimated from a Bayesian mixed model, which is robust to dealing with data imbalance and outliers. Both additive and nonadditive effects significantly influenced shoot traits, with nonadditive effects playing a larger role early in the growing season, when weed control is most critical. Results suggest the presence of heritable variation and thus potential for improvement of these phenotypes in carrot. In addition, results present evidence of heterosis for root biomass, which is a major component of carrot yield.

A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot (Daucus carota L.) Root and Petiole.

Purple carrots can accumulate large quantities of anthocyanins in their roots and -in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these "root pigmentation" regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.