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The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, su...
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... diversity analysis including 65 cultivated and wild carrots revealed valuable information on the degree of polymorphism of ten selected microsatellite loci. Table 6 presents the number of alleles (NA), allele lengths, and expected heterozygosity (H e ) found for these SSRs in our D. carota diversity collection. For this germplasm, 190 different alleles, with lengths ranging from 144 to 433 bp, were identified. ...
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... The accessibility of such markers for evaluating genetic variation is a simple way for conventional breeding to offer integrated genetic traits for breeding programs. Predefined kinds of molecular markers used for sorghum diversity evaluations became relevant, as well as they differ in complexity, reliability, and information generating capacity [22]. When genetic diversity was assessed using microsatellite (SSR) markers, a p < 0.05 of genetic variation was evidenced among 20 sorghum accessions from different agro-ecological regions in Marathwada (70% between many accessions and 30% within accessions) [19]. . ...
Allelic variation is a valuable tool for displaying high levels of polymorphism within species and is closely correlated with crop productivity. In Marathawada, there is a significant amount of phenotypic heterogeneity among sorghum landraces. However, molecular variability needs to be reevaluated in order to identify any potential barriers that can interfere with current improvement initiatives. In the current work, we used 5 SSR markers to categorize 20 genotypes of elite (Sorghum bicolor L. Moench) accession from the Marathwada region, including one standard cultivar from various agro-economic zones. According to the results of this study, 14 alleles were found among the 20 genotypes, with a PIC value that ranged from 0.37 to 0.70 and a mean of 0.44 per locus. Each locus had anything from 1 (gpsb089) and 5 (mSbCIR223), with an average of 2.80 alleles per locus. A neighbor-joining tree was constructed and showed clustering of genotypes into two groups; this indicates that there is considerable diversity in genotypes compared with advanced cultivar for desired genotype (IS1042) by using SSR markers. Results show that most diverse cultivars were IS-4564, IS18357, and IS-18381, and significant variation was also reported in IS4566 and IS18379.
... The SSRs markers developed in A. rugosa displayed higher polymorphisms than those in other crop species, which might be due to the diversity of the samples used for marker development. Using specific resources to develop SSR markers may result in markers that are genetically closer to the individuals or species used, whereas using genetically diverse resources can increase the number of marker polymorphisms (Cavagnaro et al., 2011). The plant genetic resources used in this study included local landraces and exotic lines of diverse origins ( Table 1). ...
Agastache is a genus of perennial herbaceous plants belonging to the mint family, Lamiaceae. Several Agastache species are commercially cultivated and used as medicinal, culinary, and ornamental plants. However, information on the genetic diversity and population structure of the species remains unclear. In the present study, genetic diversity within Agastache species was analyzed using simple sequence repeat (SSR) markers. In this study, 249,746 SSRs were identified in the A. rugosa genome and primer pairs were designed for 56,675 SSRs. The majority of SSR repeat types were dinucleotides (60.65%), followed by trinucleotides (12.38%), and pen-tanucleotides (12.10%). PCR conditions were established for 250 primer pairs, 111 of which were found to be polymorphic in A. rugosa germplasm. The number of alleles (N A) ranged from 2 to 19, major allele frequency (M AF) ranged from 0.11 to 0.95, observed heterozygosity (H O) ranged from 0 to 0.89, and polymorphic information content (PIC) ranged from 0.09 to 0.92. Cross-species amplification of SSRs markers in other Agastache species showed amplification rates of 82.6% for A. foeniculum and 78.1% in A. urticifolia, with an average of 80.37%. Cluster analysis of the 19 A. rugosa accessions using SSRs markers revealed four major clusters, and population STRUCTURE analysis using 79 SSRs markers revealed three groups and three subgroups among the A. rugosa populations. The SSRs markers developed can contribute to applications such as varietal identification, genetic diversity analysis, and population structure analysis of A. rugosa germplasm.
... Foliage width (crown) ranged from 10 to 55 cm with an average of 32.32 ( Table 1) Root shape was tapering (33), obtriangular (10), narrow oblong (5), wide oblong (5), obovate (13), and fusiform (3) (2), and yellow-light orange (2) (Figure 4). The different root color in carrot (D. carota) was conferred by the Y and Y2 loci in chromosomes 5 and 7, respectively, in which Y_Y2_, yyY2_, Y_y2y2, and yyy2y2 genotypes represent white, yellow, pale orange, and orange root color, respectively (Cavagnaro et al., 2011;Ellison et al., 2017). Moreover, the purple root color was due to the deposition of anthocyanin, which was regulated by the genes in the P1 and P3 regions of chromosome 3 (Bannoud et al., 2019(Bannoud et al., , 2021. ...
Abstract 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
... Finding, and the further design of, microsatellite markers for carrot enables expanding the study on different accumulation levels of carotene content in the roots and biodiversity among cultivated accessions [4,5]. The use of genomic libraries enriched with SSR repeats with further cloning in bacterial artificial chromosome (BAC) vectors led to the construction of additional 300 SSR markers [6]. The sequence analysis of the transcriptome allowed developing a set of 114 SSR markers using in silico instruments [7]. ...
... The combination of enzymes PstI/MseI for AFLP protocols was proved to reveal more polymorphism in plant objects, as was demonstrated in sorghum and corn [17]. In the study, a significant level of polymorphism (65%) was achieved that was comparable with that previously produced with highly polymorphic SSR markers in carrot [6]. Some primer evaluation parameters were shown to be higher than the average values, such as PIC and HE indices that were over 0.3, that confirms the sufficient discriminatory ability of markers. ...
It is necessary to regard the biodiversity of carrot as a genetic source of useful and indispensable components for the human diet. Amplified fragment length polymorphism (AFLP) markers were used to discriminate eight carrot genotypes with different root colors. With the combination of enzymes Tru9I, PstI, and three sets of primer pairs corresponding to adapters joint to the restricted sites, 92 loci were produced, including 60 polymorphic ones. Each of the three primer sets showed high efficiency, according to estimations of PIC (0.34, 0.34, and 0.41), D (0.36, 0.67, and 0.67), Rp (5.5, 11.3, and 15), and HE (0.32, 0.49, and 0.49). The genetic distances were calculated using values of Nei’s coefficient. The most genetically similar were Chantenay Coeur Rouge and Colmar a Coeur Rouge at a distance of 0.12, whereas the most distant were Saint Valery and Purple Dragon at the highest distance of 0.34. Confirming its genetic identity, Purple Dragon and Gelber Goliath with purple and yellow roots were the most detached varieties from others at distances of 0.23–0.34 and 0.23–0.28, respectively. Male sterile Berlicum breeding accessions were well distinct from other orange-colored varieties at the highest distance of 0.30 from Deep Purple F1. Slight modifications including the facilitation of gel staining enables the wide use of the AFLP method for genetic diversity assessment in carrot breeding accessions.
... It acts a significant role in color accumulation, growth metabolism and stress response of plant organs. Since the first MYB transcription factor C1 was found in maize, with the development of genome sequencing and bioinformatics, more and more MYB-functional genes have been studied in different species [20,[52][53][54][55]. In this study, we identified 146 R2R3-MYB factors, analyzed their phylogeny with 126 R2R3-MYB genes from A. thaliana, and divided them into 19 subfamilies. ...
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.
... SSRs also called microsatellites was one kind of molecular markers that could be detected in coding and noncoding regions of eukaryotic genomes. Compared with genomic SSRs (g-SSRs), expressed sequence tag SSRs (EST-SSRs) were developed from cDNA sequences, which located in coding regions and had more cross-species transferability (Cavagnaro et al. 2011;Zhang et al. 2006;Ellis et al. 2007). Currently, a total of 112; 2,156; 1,953; 7,235; 4,955; 5,510; 2,065 potential or putative EST-SSR had been identified from Chamaecyparis formosensis, C. lanceolata, P. densiflora, P. koraiensis, Amentotaxus formosana, Amentotaxus argotaenia, and Torreya grandis transcriptomes, respectively, and some loci were detected to be polymorphic Wen et al. 2015;Liu et al. 2015a;Li et al. 2016Li et al. , 2020cRuan et al. 2019;Zeng et al. 2018). ...
High-throughput sequencing technology has been widely used and continuously optimized. As one kind of high-throughput sequencing technology, RNA sequencing (RNA-seq) can effectively detect complete transcriptome information, which brings prospects for plant researches. Conifers are a family of Coniferopsida, mainly including Cupressaceae, Taxodiaceae, Pinaceae and Taxaceae trees. Presently, the whole genome sequencing (WGS) of many crops and broadleaf trees have been completed, while that of conifer species are limited due to huge data volume and complicated repeat sequences. Therefore, RNA-seq is one of the most important and practical methods for exploring conifers genes. This review introduced the analysis processes of RNA-seq, and highlighted the applications and prospects of RNA-seq in conifers molecular genetics, which might provide references for future genetic improvement and molecular breeding in conifer species.
... The HPLC results of wt and ym in this study were consistent with those of previous research (Figure 1). In carrots, several quantitative trait loci (QTLs) were identified to be associated with carotenoid accumulation, and the Y and Y 2 loci were firstly mapped to chromosomes 5 and 7, which explained most phenotypic variations among orange, yellow, and white storage roots [34][35][36]. DCAR_032551, the candidate gene for Y locus, was identified [6]. Y 2 was mapped within the 650 kb region, and two closely linked codominant markers, 4135 Apol1 and 4144 ApeKI , were associated with β-carotene accumulation [17]. ...
Carrots accumulate numerous carotenoids in the root, resulting in different colors. Orange carrots are primarily high in α- and β-carotene, while yellow carrots are packed with lutein. This study was designed to explore the molecular mechanism underlying the yellow mutation involving lutein using a recently obtained yellow root mutant carrot (ym) via mutagenesis of an orange root wild type (wt). Microscopes were used to observe the variations in histological and cellular structures, and transcriptome and resequencing analyses were conducted for ym and wt. The root callus of ym contained fewer colored crystals and globular chromoplasts than those of wt. Based on ribonucleic acid sequencing (RNA-seq) data analysis, 19 photosynthesis-related differentially expressed genes (DEGs) were enriched. Among them, there were 6 photosynthesis-related genes experiencing nonsynonymous mutations, including PSAL, PSB27-1, psbB, and three homologs of LHCB1.3, and Lut 5, the mapped gene regulating lutein content in carrot root, also had nonsynonymous mutations in ym. These 7 genes were shown to be significantly differently expressed at one or more time points during the lutein accumulation process. It is predicted that the 6 photosynthesis-related genes and Lut 5 are candidate genes for lutein accumulation, which results in root color mutation. The candidate genes identified in this study can provide a new insight into the molecular mechanism of lutein modulation.
... Carrots are good model plants for carotenoid research since they are rich in different carotenoids thus their taproot's color is various [15,16]. Initially, the root of a carrot was colorless ahead of domestication, and numerous breeding works brought up diverse varieties rich in carotenoids, such as anthocyanins, lycopene, α-carotene, lutein, and βcarotene [17]. ...
Studying the changes of carotenoids in the taproot of carrots under salt treatment is helpful to probe the salt stress response mechanism of carrots. The carotenoid concentration and the expression profiles of 10 carotenoid-related genes were determined in two carrot cultivars with different taproot colors. Under salt stress, the biosynthesis of carotenoids in the taproot of both ‘KRD’ and ‘BHJS’ was activated. RT-qPCR manifested that the expression levels of DcPSY1, DcPSY2, DcZDS1, DcCRT1 and DcCRT2 increased significantly in both ‘KRD’ and BHJS’ under salt stress, but DcCHXE transcripts decreased and DcPDS transcripts maintained a basal level compared to that of the control. In the taproot of ‘KRD’, the expression level of DcLCYB, DcLCYE and DcCHXB1 climbed dramatically. However, there was no significant change in the taproot of ‘BHJS’. The study showed that salt stress can stimulate the biosynthesis of carotenoids. The accumulation of lutein in the taproots of ‘KRD’ and ‘BHJS’ may be mainly attributed to the variation in DcLCYE and DcCHXB1 transcripts. The increase in β-carotene accumulation is speculated to increase salt tolerance.
... In this work, 309 clear and unambiguous bands were generated, of which 306 (99.02%) were found polymorphic, thus confirming a good level of polymorphism in the Daucus germplasm evaluated. Total polymorphic bands are higher than the value (65.1%) reported by Cavagnaro et al. (2011) with SSR markers, but in line (100%) with Baranski et al. (2012), Maksylewicz and Baranski (2013) using SSR markers, and to the value reported by Grzebelus et al. (2014) with DArT markers. Other studies on different plant species such as Adonis (Hossein-Pour et al., 2019) and Capsicum (Yildiz et al., 2020) also reported very high levels of polymorphism with iPBS markers, confirming that they are an excellent marker alternative for detecting genetic variation in plant germplasm. ...
Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that
clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity.
... Four different root colors were observed: white, yellow, orange, and purple. The different root color was conferred by the Y and Y 2 loci in the chromosomes 5 and 7, respectively, in which Y_Y 2 _, yyY 2 _, Y_y 2 y 2 , and yyy 2 y 2 genotypes represent white, yellow, pale orange, and orange root color, respectively [38,39]. Moreover, the purple root color was due to the deposition of anthocyanin, which was regulated by the genes in the P 1 and P 3 regions of chromosome 3 [40,41]. ...
Carrot (Daucus carota), one of the most economically important root vegetables, shows a wide range of morphological and biochemical diversity. However, there is a lack of simultaneous systematic study regarding the biochemical composition and morphological characteristics in carrot genetic resources, which is crucial for crop improvement. For this reason, the morphological characteristics, carotenoids, and free sugar content of 180 carrot genetic resources grown in open field conditions from March to June 2020 were accessed to select the lines for a potential breeding program. Altogether, 15 qualitative and 4 quantitative agronomical characteristics were evaluated and grouped into four categories based on root color (orange, yellow, white, and purple). Three carotenoids (lutein, α-carotene, and β-carotene) and three free sugars (fructose, glucose, and sucrose) were also analyzed. The results revealed wide genetic variation in both qualitative and quantitative traits. Most of the genetic resources were orange (n = 142), followed by white (n = 16), yellow (n = 14), and purple (n = 8). Carotenoid profile and content were highly dependent on root color and showed wide genetic variability, while sugar content and profile were independent of the root color. Alpha- and β- carotene were the major carotenoids in orange carrots representing 43.3 and 41.0% of total carotenoids. In contrast, lutein was most dominant in other colored carrots (79.7–98.6% of total carotenoids). In most of the genetic resources, sucrose was the most dominant free sugar, followed by glucose and fructose. The results of this study showed that some genetic resources elevated carotenoid and sugar content. The morphological and biochemical diversity observed in this study might be useful for improving the agronomic traits and biochemical content of carrot lines for breeding programs.
