Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population

Effects of ultrasound and microwave pretreatments of carrot slices before drying on the color indexes and drying rate

The aim of this study was to examine the impacts of microwave pretreatment (MWP) and ultrasonic pretreatment (USP) on drying time (DT), mass transfer kinetics, effective water diffusivity (Deff), rehydration rate, color index (L*, a*, b*), and the surface shrinkage of carrot slices when dried in a hot air dryer (70 °C). The microwave process was performed for 0, 15, 30, 45, and 60 s before drying of carrot slices. In addition, the ultrasound process was performed in an ultrasonic bath (40 kHz and 150 W) for 0, 5, 10, 15, and 20 min. The results confirmed that the MWP and USP decreased the DT (higher water loss) of carrot slices. Deff values for microwave-pretreated slices were considerably higher than those for nontreated carrot slices (p < 0.05). The Deff calculated by Fick's second law was increased from 8.69 × 10-10 to 10.96 × 10-10 m2 s-1, and from 7.56 × 10-10 to 9.39 × 10-10 m2 s-1, for samples pretreated by microwave and ultrasound, respectively. The empirical value for the drying curves were fitted to the common thin film-equations, and Page's equation was the most suitable to describe the dehydration rate of carrot slices. The average rehydration ratio of nontreated, microwave-treated, and ultrasound-treated carrot slices were 432.3 %, 449.2 %, and 360.9 %, respectively. The redness, yellowness, and surface shrinkage parameters of pretreated samples by microwave were higher than the nontreated slices. The lightness and redness parameters of pretreated carrot slices by ultrasound were higher than the nontreated samples under all conditions.

Lycopene ε-cyclase mediated transition of α-carotene and β-carotene metabolic flow in carrot fleshy root

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.

Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies

BACKGROUND

Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene-the main provitamin A carotenoid-is below the target concentration in sorghum grain, therefore biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors.

RESULTS

In this study, we characterized carotenoids in 446 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies conducted with 345 accessions, confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin, but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity, and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts.

CONCLUSIONS

Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus pre-breeding will be needed. A SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.

Influence of Root Color and Tissue on Phytochemical Contents and Antioxidant Activities in Carrot Genotypes

This study monitored changes in major carotenoids (lutein, ⍺-carotene, and β-carotene), free sugars (fructose, glucose, and sucrose), ascorbic acid, vitamin E, phytosterols (campesterol, stigmasterol, and β-sitosterol), fatty acid composition, total phenol content (TPC), total flavonoid content (TFC), total anthocyanin content, and antioxidant activities (AA); ferric-reducing antioxidant power (FRAP) and 2,2'-azino-bis (3-ethylbenzothiazoline-6sulfonic acid) [ABTS] assays, in the inner and outer root tissues of nine carrot genotypes with orange, white, and purple roots. The results showed a differential accumulation of bioactive compounds and antioxidant activities depending on root tissue and color. Carotenoids, free sugars, and total phytosterol contents were higher in genotypes with orange roots than in other genotypes. Ascorbic acid, TPC, TFC, total anthocyanin, and AA were highest in purple-colored carrots while vitamin E content was higher in white/purple carrots. Root color was highly related to the accumulation of individual carotenoids, vitamin E isomers, and total anthocyanin content most prominently among the analyzed bioactive compounds and AA. Free sugar and carotenoid contents were relatively higher in outer tissues than in inner tissues. Furthermore, ascorbic acid, TPC, TFC, and AA were statistically higher or similar in outer tissues when compared to inner tissues in all genotypes. In contrast, trends in vitamin E and phytosterol content were inconsistent between the inner and outer tissues, depending on the genotype. Although fatty acid composition was affected by both root color and tissue, the results were not significant. Thus, the phytochemical profile and content were highly dependent on root color and tissue in carrot genotypes. This may be useful in the food processing and pharmaceutical industries for the extraction of targeted bioactive compounds.

Plastid diversity and chromoplast biogenesis in differently coloured carrots: role of the DcOR3Leu gene

Distinct plastid types and ultrastructural changes are associated with differences in carotenoid pigment profiles in differently coloured carrots, and a variant of the OR gene, DcOR3^Leu is vital for chromoplast biogenesis. Accumulation of different types and amounts of carotenoids in carrots impart different colours to their taproots. In this study, the carotenoid pigment profiles, morphology, and ultrastructure of plastids in 25 carrot varieties with orange, red, yellow, or white taproots were investigated by ultra-high performance liquid chromatography as well as light and transmission electron microscopy. α-/β-Carotene and lycopene were identified as colour-determining carotenoids in orange and red carrots, respectively. In contrast, lutein was identified as the colour-determining carotenoid in almost all tested yellow and white carrots. The latter contained only trace amounts of lutein as a unique detectable carotenoid. Striking differences in plastid types that coincided with distinct carotenoid profiles were observed among the differently coloured carrots. Microscopic analysis of the different carotenoid pigment-loaded plastids revealed abundant crystalloid chromoplasts in the orange and red carrots, whereas amyloplasts were dominant in most of the yellow and white carrots, except for the yellow carrot 'Yellow Stone', where yellow chromoplasts were observed. Plastoglobuli and crystal remnants, the carotenoid sequestering substructures, were identified in crystalloid chromoplasts. Crystal remnants were often associated with a characteristic undulated internal membrane in orange carrots or several undulated membranes in red carrots. No crystal remnants, but some plastoglobuli, were observed in the plastids of all tested yellow and white carrots. In addition, the presence of chromoplast in carrot taproots was found to be associated with DcOR3^Leu, a natural variant of DcOR3, which was previously reported to be co-segregated with carotene content in carrots. Knocking out DcOR3^Leu in the orange carrot 'Kurodagosun' depressed chromoplast biogenesis and led to the generation of yellow carrots. Our results support that DcOR3^Leu is vital but insufficient for chromoplasts biogenesis in carrots, and add to the understanding of the formation of chromoplasts in carrots.

Green extraction of bioactive components from carrot industry waste and evaluation of spent residue as an energy source

Carrot processing industries produce 25-30% of waste in the form of carrot rejects, peels, and pomace which contain a large amount of high-value bioactive components. Green extraction of the bioactive components from carrot rejects with green solvents using closed-vessel energy-intensive microwave-assisted extraction was the objective of this work. In this work, three experimental studies were implemented. One uses 8 different green solvents for maximum yield of bioactive using green technology, and the other for the optimization of Microwave-assisted Extraction (MAE) parameters to enhance the bioactive components yield. Response Surface Methodology was employed to optimize the processing parameters including temperature, time, solid to solvent ratio, and solvent type. The optimized extraction conditions: treatment temperature of 50 °C for 5 min gave a significantly higher yield of total carotenoids (192.81 ± 0.32 mg carotenoids/100 g DW), total phenolic (78.12 ± 0.35 g GAE/100 g DW), and antioxidants by FRAP (5889.63 ± 0.47 mM TE/100 g DW), ABTS (1143.65 ± 0.81 mM TE/100 g DW), and DPPH (823.14 ± 0.54 mM TE/100 g DW) using a solvent combination of hexane and ethanol (1:3) with solid to solvent ratio of 1:40 (w/v). This green technology in combination with GRAS solvents promoted the best recovery of bioactive from carrot rejects. Moreover, the solid residue remained after the extraction of bioactive components exhibited higher carbon content (46.5%) and calorific value (16.32 MJ/kg), showcasing its potential to be used as an energy source.

Correlation of Carotenoids Content and ASTA Values of Pepper (Capsicum chinense) Genetic Resources

In this study, 226 Capsicum chinense genetic resources were analyzed using high-performance liquid chromatography and a spectrophotometer to measure and compare their carotenoid content and American Spice Trade Association (ASTA) color values, respectively. The total carotenoid content and ASTA values of the 226 pepper genetic resources were found to be in the range of 7.04–2430.85 mg/100 g dry weight (DW) and 0–221.32, respectively. Capsanthin, capsorubin, lutein, zeaxanthin, antheraxanthin, violaxanthin, α-carotene, β-carotene, and β-cryptoxanthin were the individual carotenoids studied. The average content of each carotenoid (n = 226) in mg/100 g DW was as follows: capsanthin (325.77), antheraxanthin (136.34), capsorubin (82.36), β-carotene (59.11), violaxanthin (46.54), zeaxanthin (43.21), α-carotene (13.91), β-cryptoxanthin (9.67), and lutein (2.72). A strong positive correlation was observed between total carotenoid content and ASTA value (r = 0.965). Likewise, the individual carotenoid content and ASTA value revealed a strong correlation, such as antheraxanthin (r = 0.964), capsanthin (r = 0.946), and capsorubin (r = 0.858). Three genetic resources with a total carotenoid content above 2000 mg/100 g DW were obtained, such as IT261426 (2430.85 mg/100 g DW), IT183657 (2077.55 mg/100 g DW), and IT261213 (2062.54 mg/100 g DW). The findings of this study will assist in the selection of genetic resources with high carotenoid content and ASTA value that can be used to develop and breed new pepper varieties. Also, detailed results of ASTA value correlation with carotenoids in C. chinense genetic resources are provided.

Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F2 populations

Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

Omics Technologies to Enhance Plant Based Functional Foods: An Overview

Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.

Multisite evaluation of phenotypic plasticity for specialized metabolites, some involved in carrot quality and disease resistance

Renewed consumer demand motivates the nutritional and sensory quality improvement of fruits and vegetables. Specialized metabolites being largely involved in nutritional and sensory quality of carrot, a better knowledge of their phenotypic variability is required. A metabolomic approach was used to evaluate phenotypic plasticity level of carrot commercial varieties, over three years and a wide range of cropping environments spread over several geographical areas in France. Seven groups of metabolites have been quantified by HPLC or GC methods: sugars, carotenoids, terpenes, phenolic compounds, phenylpropanoids and polyacetylenes. A large variation in root metabolic profiles was observed, in relation with environment, variety and variety by environment interaction effects in decreasing order of importance. Our results show a clear diversity structuration based on metabolite content. Polyacetylenes, β-pinene and α-carotene were identified mostly as relatively stable varietal markers, exhibiting static stability. Nevertheless, environment effect was substantial for a large part of carrot metabolic profile and various levels of phenotypic plasticity were observed depending on metabolites and varieties. A strong difference of environmental sensitivity between varieties was observed for several compounds, particularly myristicin, 6MM and D-germacrene, known to be involved in responses to biotic and abiotic stress. This work provides useful information about plasticity in the perspective of carrot breeding and production. A balance between constitutive content and environmental sensitivity for key metabolites should be reached for quality improvement in carrot and other vegetables.

Functional relationship of vegetable colors and bioactive compounds: Implications in human health

Vegetables are essential protective diet ingredients that supply ample amounts of minerals, vitamins, carbohydrates, proteins, dietary fiber, and various nutraceutical compounds for protection against various disease conditions. Color is the most important quality parameter for the farmers to access the harvest maturity while for the consumer's reliable indices to define acceptability or rejection. The colored vegetables contain functional compounds like chlorophylls, carotenoids, betalains, anthocyanins, etc. well recognized for their antioxidant, antimicrobial, hypolipidemic, neuroprotective, antiaging, diuretic, and antidiabetic properties. Recently, there has been a shift in food consumption patterns from processed to semi-processed or fresh fruits and vegetables to ensure a healthy disease-free life. This shifted the focus of agriculture scientists and food processors from food security to nutrition security. This has resulted in recent improvements to existing crops like blue tomato, orange cauliflower, colored and/or black carrots, with improved color, and thus enriched bioactive compounds. Exhaustive laboratory trials though are required to document and establish their minimum effective concentrations, bioavailability, and specific health benefits. Efforts should also be directed to breed color-rich cultivars or to improve the existing varieties through conventional and molecular breeding approaches. The present review has been devoted to a better understanding of vegetable colors with specific health benefits and to provide in-hand information about the effect of specific pigment on body organs, the effect of processing on their bioavailability, and recent improvements in colors to ensure a healthy lifestyle.

Feeding unsaleable carrots to lambs increased performance and carcass characteristics while maintaining meat quality

This study investigated the effect of feeding unsaleable carrots to lambs within a total-mixed ration (TMR) on performance, carcass characteristics, meat quality and sensory parameters. Thirty-six Australian Merino wether lambs were fed a control (barley-based) or carrot-based TMR for 11-weeks. Carrot-fed lambs had 2.7% higher cold dressing percentage (P = 0.03) while consuming less than control lambs. Subcutaneous fat of carrot-fed lambs contained less branch-chained, and more cis- and trans-monounsaturated fatty acids (FA; P ≤ 0.01) compared to control-fed lambs, which tended (P = 0.08) to have higher concentrations of polyunsaturated FA, despite the Longissimus lumborum (LL) muscle being unchanged by diet. Under retail display conditions, L* and hue values were lower (P ≤ 0.04) for 5 d aged LL samples from carrot-fed lambs. No differences were observed in other meat quality and sensory parameters between diets. Therefore, feeding unsaleable carrots at 45% DM in a TMR can improve lamb performance and carcass characteristics, while maintaining meat quality and FA composition.

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.

Transcript profiling of genes involved in carotenoid biosynthesis among three carrot cultivars with various taproot colors

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.

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 F_st , 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.

Effect of smear layer deproteinization on bonding of self-etch adhesives to dentin: a systematic review and meta-analysis

OBJECTIVES

The aim of this systematic review was to critically analyze previously published studies of the effects of dentin surface pretreatment with deproteinizing agents on the bonding of self-etch (SE) adhesives to dentin. Additionally, a meta-analysis was conducted to quantify the effects of the above-mentioned surface pretreatment methods on the bonding of SE adhesives to dentin.

MATERIALS AND METHODS

An electronic search was performed using the following databases: Scopus, PubMed and ScienceDirect. The online search was performed using the following keywords: 'dentin' or 'hypochlorous acid' or 'sodium hypochlorite' and 'self-etch adhesive.' The following categories were excluded during the assessment process: non-English articles, randomized clinical trials, case reports, animal studies, and review articles. The reviewed studies were subjected to meta-analysis to quantify the effect of the application time and concentration of sodium hypochlorite (NaOCl) and hypochlorous acid (HOCl) deproteinizing agents on bonding to dentin.

RESULTS

Only 9 laboratory studies fit the inclusion criteria of this systematic review. The results of the meta-analysis revealed that the pooled average microtensile bond strength values to dentin pre-treated with deproteinizing agents (15.71 MPa) was significantly lower than those of the non-treated control group (20.94 MPa).

CONCLUSIONS

In light of the currently available scientific evidence, dentin surface pretreatment with deproteinizing agents does not enhance the bonding of SE adhesives to dentin. The HOCl deproteinizing agent exhibited minimal adverse effects on bonding to dentin in comparison with NaOCl solutions.

Antioxidant Phytochemicals in Fresh Produce: Exploitation of Genotype Variation and Advancements in Analytical Protocols

Horticultural commodities (fruit and vegetables) are the major dietary source of several bioactive compounds of high nutraceutical value for humans, including polyphenols, carotenoids and vitamins. The aim of the current review was dual. Firstly, toward the eventual enhancement of horticultural crops with bio-functional compounds, the natural genetic variation in antioxidants found in different species and cultivars/genotypes is underlined. Notably, some landraces and/or traditional cultivars have been characterized by substantially higher phytochemical content, i.e., small tomato of Santorini island (cv. "Tomataki Santorinis") possesses appreciably high amounts of ascorbic acid (AsA). The systematic screening of key bioactive compounds in a wide range of germplasm for the identification of promising genotypes and the restoration of key gene fractions from wild species and landraces may help in reducing the loss of agro-biodiversity, creating a healthier "gene pool" as the basis of future adaptation. Toward this direction, large scale comparative studies in different cultivars/genotypes of a given species provide useful insights about the ones of higher nutritional value. Secondly, the advancements in the employment of analytical techniques to determine the antioxidant potential through a convenient, easy and fast way are outlined. Such analytical techniques include electron paramagnetic resonance (EPR) and infrared (IR) spectroscopy, electrochemical, and chemometric methods, flow injection analysis (FIA), optical sensors, and high resolution screening (HRS). Taking into consideration that fruits and vegetables are complex mixtures of water- and lipid-soluble antioxidants, the exploitation of chemometrics to develop "omics" platforms (i.e., metabolomics, foodomics) is a promising tool for researchers to decode and/or predict antioxidant activity of fresh produce. For industry, the use of optical sensors and IR spectroscopy is recommended to estimate the antioxidant activity rapidly and at low cost, although legislation does not allow its correlation with health claims.

Fine Mapping, Transcriptome Analysis, and Marker Development for Y2 , the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.)

Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y2 Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot.

Quantitative trait loci from identification to exploitation for crop improvement

Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.

Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust

KEY MESSAGE

Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown. To address these questions, a set of 1035 genome-wide single nucleotide polymorphisms (SNPs) was associated to the quantitative variation of four simple phenylpropanoids, eight stilbenes, nine flavonoids, six related arithmetic parameters and the susceptibility to infection by Chrysomyxa rhododendri in an unstructured natural population of Norway spruce. Thirty-one significant genetic associations for the flavonoids gallocatechin, kaempferol 3-glucoside and quercetin 3-glucoside and the stilbenes resveratrol, piceatannol, astringin and isorhapontin were discovered, explaining 22-59% of phenotypic variation, and indicating a regulation of phenolic accumulation by many genes with small and additive effects. The phenolics profile differed between trees with high and low susceptibility to the fungus, underlining the importance of phenolic compounds in the defence mechanisms of Norway spruce to C. rhododendri. Results highlight the utility of association studies in non-model tree species and may enable marker-assisted selection of Norway spruce adapted to severe pathogen attack.

Carotenoid gene expression explains the difference of carotenoid accumulation in carrot root tissues

Main conclusion Variations in gene expression can partially explain the difference of carotenoid accumulation in secondary phloem and xylem of fleshy carrot roots. The carrot root is well divided into two different tissues separated by vascular cambium: the secondary phloem and xylem. The equilibrium between these two tissues represents an important issue for carrot quality, but the knowledge about the respective carotenoid accumulation is sparse. The aim of this work was (i) to investigate if variation in carotenoid biosynthesis gene expression could explain differences in carotenoid content in phloem and xylem tissues and (ii) to investigate if this regulation is differentially modulated in the respective tissues by water-restricted growing conditions. In this work, five carrot genotypes contrasting by their root color were studied in control and water-restricted conditions. Carotenoid content and the relative expression of 13 genes along the carotenoid biosynthesis pathway were measured in the respective tissues. Results showed that in orange genotypes and the purple one, carotenoid content was higher in phloem compared to xylem. For the red one, no differences were observed. Moreover, in control condition, variations in gene expression explained the different carotenoid accumulations in both tissues, while in water-restricted condition, no clear association between gene expression pattern and variations in carotenoid content could be detected except in orange-rooted genotypes. This work shows that the structural aspect of carrot root is more important for carotenoid accumulation in relation with gene expression levels than the consequences of expression changes upon water restriction.

Exogenous gibberellin enhances secondary xylem development and lignification in carrot taproot

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 GA₃. The effects of applied GA₃ 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 GA₃ treatment. Moreover, lignin content increased in the roots, and the transcripts of lignin biosynthesis genes were altered in response to applied GA₃. 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.

Down the Rabbit Hole-Carrots, Genetics and Art

The recent carrot genome assembly provides insight into carotenoid accumulation in carrots, and allows-together with other genetic information-to provide a molecular explanation for color differences observed in carrots painted throughout the centuries.

ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed

Elucidation of the carotenoid biosynthetic pathway has enabled altering the composition and content of carotenoids in various plants, but to achieve desired nutritional impacts, the genetic components regulating carotenoid homeostasis in seed, the plant organ consumed in greatest abundance, must be elucidated. We used a combination of linkage mapping, genome-wide association studies (GWAS), and pathway-level analysis to identify nine loci that impact the natural variation of seed carotenoids in Arabidopsis (Arabidopsis thaliana). ZEAXANTHIN EPOXIDASE (ZEP) was the major contributor to carotenoid composition, with mutants lacking ZEP activity showing a remarkable 6-fold increase in total seed carotenoids relative to the wild type. Natural variation in ZEP gene expression during seed development was identified as the underlying mechanism for fine-tuning carotenoid composition, stability, and ultimately content in Arabidopsis seed. We previously showed that two CAROTENOID CLEAVAGE DIOXYGENASE enzymes, CCD1 and CCD4, are the primary mediators of seed carotenoid degradation, and here we demonstrate that ZEP acts as an upstream control point of carotenoid homeostasis, with ZEP-mediated epoxidation targeting carotenoids for degradation by CCD enzymes. Finally, four of the nine loci/enzymatic activities identified as underlying natural variation in Arabidopsis seed carotenoids also were identified in a recent GWAS of maize (Zea mays) kernel carotenoid variation. This first comparison of the natural variation in seed carotenoids in monocots and dicots suggests a surprising overlap in the genetic architecture of these traits between the two lineages and provides a list of likely candidates to target for selecting seed carotenoid variation in other species.

Differential Pigment Accumulation in Carrot Leaves and Roots during Two Growing Periods

Carotenoids are important secondary metabolites involved in plant growth and nutritional quality of vegetable crops. These pigments are highly accumulated in carrot root, but knowledge about the impact of environmental factors on their accumulation is limited. The purpose of this work was to investigate the impact of environmental variations on carotenoid accumulation in carrot leaves and roots. In this work, carrots were grown during two contrasting periods to maximize bioclimatic differences. In leaves, carotenoid and chlorophyll contents were lower in the less favorable growing conditions, whereas relative contents were well conserved for all genotypes, suggesting a common regulatory mechanism. The down-regulation of all genes under environmental constraints demonstrates that carotenoid accumulation is regulated at the transcriptional level. In roots, the decrease in α-carotene and lutein contents was accompanied by an increase of β-carotene relative content. At the transcriptional level, LCYB and ZEP expression increased, whereas LCYE expression decreased, in the less favorable conditions, suggesting that carotenoid biosynthesis is switched toward the β-branch.