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

Genetic architecture of anthocyanin pigment traits and purple spot (Stemphylium vesicarium) resistance in an F1 pseudo-testcross population of asparagus

Stemphylium vesicarium (Wallr.) Simmons is a plant pathogenic fungus causing purple spot in both fern and spears of asparagus (Asparagus officinalis L.). Although the fern can be sprayed with fungicides to control the disease, pesticide applications during spear harvest are restricted. Infected spears can develop prominent pigmentation at lesion sites, reducing marketable yield. Breeding resistant asparagus cultivars with decreased lesion numbers and reduced purpling at the site of infection is considered the most economical and sustainable approach to combat this disease. The objectives of this study were to determine the genetic architectures of, and relationships among, anthocyanin pigment expression in spear scale leaves (ALS) and spear lesions (APS) and purple spot levels in spears (NPS) and fern (PSF). Traits were phenotyped over 2 years under natural conditions in an F1 pseudo-testcross population, and quantitative trait loci (QTL) were mapped. ALS, APS, NPS, and PSF were not correlated, suggesting independent regulation of the anthocyanin pathway in scale leaves and lesions and no relationship between pigment and disease. Segregation, 3 red:1 purple and 3 red:13 purple, was observed in scale leaves and lesions, respectively. Two stable QTL for each of ASL, APS, and NPS, one tentative QTL for ASL, four tentative QTL for APS, two tentative QTL for NPS, and three tentative QTL for PSF were identified. Candidate genes were found for four loci. This study advances the genetic understanding of anthocyanin pigmentation at a tissue-specific level, and purple spot disease severity in spears and fern, supporting future breeding efforts.

Population structure, genetic diversity, and GWAS analyses with GBS-derived SNPs and silicodart markers unveil genetic potential for breeding and candidate genes for agronomic and root quality traits in an international sugar beet germplasm collection

BACKGROUND

Knowledge about the degree of genetic diversity and population structure is crucial as it facilitates novel variations that can be used in breeding programs. Similarly, genome-wide association studies (GWAS) can reveal candidate genes controlling traits of interest. Sugar beet is a major industrial crops worldwide, generating 20% of the world's total sugar production. In this work, using genotyping by sequencing (GBS)-derived SNP and silicoDArT markers, we present new insights into the genetic structure and level of genetic diversity in an international sugar beet germplasm (94 accessions from 16 countries). We also performed GWAS to identify candidate genes for agriculturally-relevant traits.

RESULTS

After applying various filtering criteria, a total of 4,609 high-quality non-redundant SNPs and 6,950 silicoDArT markers were used for genetic analyses. Calculation of various diversity indices using the SNP (e.g., mean gene diversity: 0.31, MAF: 0.22) and silicoDArT (mean gene diversity: 0.21, MAF: 0.12) data sets revealed the existence of a good level of conserved genetic diversity. Cluster analysis by UPGMA revealed three and two distinct clusters for SNP and DArT data, respectively, with accessions being grouped in general agreement with their geographical origins and their tap root color. Coincidently, structure analysis indicated three (K = 3) and two (K = 2) subpopulations for SNP and DArT data, respectively, with accessions in each subpopulation sharing similar geographic origins and root color; and comparable clustering patterns were also found by principal component analysis. GWAS on 13 root and leaf phenotypic traits allowed the identification of 35 significant marker-trait associations for nine traits and, based on predicted functions of the genes in the genomic regions surrounding the significant markers, 25 candidate genes were identified for four root (fresh weight, width, length, and color) and three leaf traits (shape, blade color, and veins color).

CONCLUSIONS

The present work unveiled conserved genetic diversity-evidenced both genetically (by SNP and silicoDArT markers) and phenotypically- exploitable in breeding programs and germplasm curation of sugar beet. Results from GWAS and candidate gene analyses provide a frame work for future studies aiming at deciphering the genetic basis underlying relevant traits for sugar beet and related crop types within Beta vulgaris subsp. vulgaris.

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

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

Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots

Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.

Morphological characterizations of parsnip (Pastinaca sativa L.) to select superior genotypes

Parsnip (Pastinaca sativa L.) is an edible root that has long been used in cooking and preparing baby food and livestock. The present study was performed to evaluate the phenotypic diversity of 69 accessions of this species to select superiors in terms of root quality in Paykan village, Isfahan province, Iran, in the year 2022. There were significant differences among the accessions investigated (ANOVA, p < .01). Coefficient of variation (CV) was more than 20.00% in the majority of measured characters (64 out of 66 characters), indicating high diversity among the accessions. Foliage width (crown) ranged from 10 to 55 cm with an average of 32.32 cm. Root shape was tapering (33), obtriangular (10), narrow oblong (5), wide oblong (5), obovate (13), and fusiform (3). Root length ranged from 81.2 to 294 mm with an average of 166.44 mm. Root diameter at its middle point ranged from 15.58 to 125.12 mm with an average of 51.83 mm. Root weight ranged from 15 to 1200 g with an average of 315.36 g. Inner core (xylem) pigmentation/color was cream yellow (11 accessions), light yellow (12), yellow (42), dark yellow (2), and yellow-light orange (2). In the cluster analysis based on Ward's method, the accessions were divided into two main clusters according to morphological traits. This is despite the fact that parsnip is part of the medicinal plant native and valuable in most farms in tropical cities. Compared with carrots, parsnip plants are more adaptable to different environmental conditions. The accessions studied here showed high phenotypic diversity. Based on ideal values of the important and commercial characters of parsnip, such as root length, root weight, inner core (xylem) pigmentation/color, root shape, flesh color intensity, flesh palatability, and total soluble solids, 14 genotypes, including Parsnip-3, Parsnip-9, Parsnip-24, Parsnip-32, Parsnip-32, Parsnip-48, Parsnip-51, Parsnip-52, Parsnip-58, Parsnip-60, Parsnip-62, Parsnip-65, Parsnip-67, and Parsnip-69, were promising and are recommended for cultivation.

Genome-wide identification of MATE, functional analysis and molecular dynamics of DcMATE21 involved in anthocyanin accumulation in Daucus carota

Anthocyanins are a subclass of flavonoids that are synthesized in the endoplasmic reticulum and then transported to the vacuole in plants. Multidrug and toxic compound extrusion transporters (MATE) is a family of membrane transporters that transport ions and secondary metabolites, such as anthocyanins, in plants. Although various studies on MATE transporters have been carried out on different plant species, this is the first comprehensive report to mine the Daucus carota genome to identify the MATE gene family. Our study identified 45 DcMATEs through genome-wide analysis and detected five segmental and six tandem duplications from the genome. The chromosome distribution, phylogenetic analysis, and cis-regulatory elements revealed the structural diversity and numerous functions associated with the DcMATEs. In addition, we analyzed RNA-seq data obtained from the European Nucleotide Archive to screen for the expression of DcMATEs involved in anthocyanin biosynthesis. Among the identified DcMATEs, DcMATE21 correlated with anthocyanin content in the different D. carota varieties. In addition, the expression of DcMATE21 and anthocyanin biosynthesis genes was correlated under abscisic acid, methyl jasmonate, sodium nitroprusside, salicylic acid, and phenylalanine treatments, which were substantiated by anthocyanin accumulation in the in vitro cultures. Further molecular membrane dynamics of DcMATE21 with anthocyanin (cyanidin-3-glucoside) identified the binding pocket, showing extensive H-bond interactions with 10 crucial amino acids present in the transmembrane helix of 7, 8, and 10 of DcMATE21. The current investigation, using RNA-seq, in vitro cultures, and molecular dynamics studies revealed the involvement of DcMATE21 in anthocyanin accumulation in vitro cultures of D. carota.

Generating colorful carrot germplasm through metabolic engineering of betalains pigments

Betalains are tyrosine-derived plant pigments exclusively found in the Caryophyllales order and some higher fungi and generally classified into two groups: red-violet betacyanins and yellow-orange betaxanthins. Betalains attract great scientific and economic interest because of their relatively simple biosynthesis pathway, attractive colors and health-promoting properties. Co-expressing two core genes BvCYP76AD1 and BvDODA1 with or without a glycosyltransferase gene MjcDOPA5GT allowed the engineering of carrot (an important taproot vegetable) to produce a palette of unique colors. The highest total betalains content, 943.2 μg·g-1 DW, was obtained in carrot taproot transformed with p35S:RUBY which produces all of the necessary enzymes for betalains synthesis. Root-specific production of betalains slightly relieved tyrosine consumption revealing the possible bottleneck in betalains production. Furthermore, a unique volcano-like phenotype in carrot taproot cross-section was created by vascular cambium-specific production of betalains. The betalains-fortified carrot in this study is thus anticipated to be used as functional vegetable and colorful carrot germplasm in breeding to promote health.

Differential and Cultivar-Dependent Antioxidant Response of Whole and Fresh-Cut Carrots of Different Root Colors to Postharvest UV-C Radiation

Fresh-cut produce have become widely popular, increasing vegetable consumption in many parts of the word. However, they are more perishable than unprocessed fresh vegetables, requiring cold storage to preserve their quality and palatability. In addition to cold storage, UV radiation has been used experimentally to try to increase nutritional quality and postharvest shelf life, revealing increased antioxidant levels in some fruits and vegetables, including orange carrots. Carrot is one of the main whole and fresh-cut vegetables worldwide. In addition to orange carrots, other root color phenotypes (e.g., purple, yellow, red) are becoming increasingly popular in some markets. The effect of the UV radiation and cold storage has not been explored in these root phenotypes. This study investigated the effect of postharvest UV-C radiation in whole and fresh-cut (sliced and shredded) roots of two purple, one yellow, and one orange-rooted cultivar, with regard to changes in concentration of total phenolics (TP) and hydroxycinnamic acids (HA), chlorogenic acid (CGA), total and individual anthocyanins, antioxidant capacity (by DPPH and ABTS), and superficial color appearance, monitoring such changes during cold storage. Results revealed that the UV-C radiation, the fresh-cut processing, and the cold storage influenced the content of antioxidant compounds and activities to varying extents, depending on the carrot cultivar, the degree of processing, and the phytochemical compound analyzed. UV-C radiation increased antioxidant capacity up to 2.1, 3.8, 2.5-folds; TP up to 2.0, 2.2, and 2.1-folds; and CGA up to 3.2, 6.6, and 2.5-folds, relative to UV-C untreated controls, for orange, yellow, and purple carrots, respectively. Anthocyanin levels were not significantly modified by the UV-C in both purple carrots evaluated. A moderate increase in tissue browning was found in some fresh-cut processed UV-C treated samples of yellow and purple but not orange roots. These data suggest variable potential for increasing functional value by UV-C radiation in different carrot root colors.

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.

Genome-Wide Identification and Evolution Analysis of R2R3-MYB Gene Family Reveals S6 Subfamily R2R3-MYB Transcription Factors Involved in Anthocyanin Biosynthesis in Carrot

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

A Survey of Enhanced Cold Tolerance and Low-Temperature-Induced Anthocyanin Accumulation in a Novel Zoysia japonica Biotype

Zoysia japonica is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of Z. japonica can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel Z. japonica biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular Z. japonica cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of Phenylalanine ammonia-lyase (PAL), Homeobox-leucine Zipper IV (HD-ZIP), and ATP-Binding Cassette transporter B8 (ABCB8) expressions, as well as a unique down-regulation of zinc-regulated transporters and iron-regulated transporter-like proteins (ZIPs) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant Z. japonica variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.

Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines

Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota "Songzi" and the orange cultivar "Amsterdam forcing" was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC₂F₁ plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4-66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.