Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products

Rapid and sensitive approaches for detecting food fraud: A review on prospects and challenges

Precise and reliable analytical techniques are required to guarantee food quality in light of the expanding concerns regarding food safety and quality. Because traditional procedures are expensive and time-consuming, quick food control techniques are required to ensure product quality. Various analytical techniques are used to identify and detect food fraud, including spectroscopy, chromatography, DNA barcoding, and inotrope ratio mass spectrometry (IRMS). Due to its quick findings, simplicity of use, high throughput, affordability, and non-destructive evaluations of numerous food matrices, NI spectroscopy and hyperspectral imaging are financially preferred in the food business. The applicability of this technology has increased with the development of chemometric techniques and near-infrared spectroscopy-based instruments. The current research also discusses the use of several multivariate analytical techniques in identifying food fraud, such as principal component analysis, partial least squares, cluster analysis, multivariate curve resolutions, and artificial intelligence.

Morphological, biochemical and molecular characterization of short-day tropical Indian garlic (Allium sativum L.)

Garlic, an asexually propagated bulbous crop, displays a wide diversity based on its morphological traits and biochemical compositions. This study investigated the genetic variability of Indian garlic through morphological, biochemical, and molecular markers. Twenty-nine genotypes along with three Allium species as outgroup were included in the present study. Observations were recorded on 14 quantitative traits, 17 qualitative traits, and 9 biochemical traits in fresh garlic. Significant variability was observed among genotypes for different characters. All the morphological and biochemical traits showed higher phenotypic coefficient of variation (PCV) than genotypic coefficient of variation (GCV) revealing the role of environment in trait expression. High to moderate heritability and genetic advance as percent mean were recorded for different traits except dry matter and Total Soluble Solids (TSS). Correlation analysis revealed the highest positive correlation between total yield, marketable yield, Ferric Reducing Antioxidant Potential (FRAP) and 2,2-diphenyl-1-picrylhyrazyl (DPPH). Cluster analysis differentiated all the genotypes into three major clusters based on morphological and biochemical traits. 214 Simple Sequence Repeats (SSRs) were screened and nine markers exhibited polymorphism. Cluster analysis using molecular markers revealed 4 distinct clusters. The observations from this study will help in the identification of diverse garlic germplasm for its efficient management and duplicate identification of germplasm resources.

Varietal identification in pasta through an SSR-based approach: a case study

BACKGROUND

Pasta is a worldwide popular Italian food made exclusively of durum wheat. The choice of variety to be used to produce pasta is at the discretion of the producer based on the peculiar characteristics of each cultivar. The availability of analytical approaches for the tracking of specific varieties along the productive chain is becoming increasingly important to authenticate the pasta products and distinguish between fraudulent activities and cross-contaminations during the production process. Among the different methods, molecular approaches based on DNA markers are the most used for these purposes because of their ease of use and high reproducibility.

RESULTS

In the present study, we used an easy simple sequence repeats-based method to identify the durum wheat varieties used to produce 25 samples of semolina and commercial pasta comparing their molecular profile with those of the four varieties declared by the producer and other 10 durum wheat cultivars commonly used in pasta production. All of the samples showed the expected molecular profile; however, most of them present also a foreign allele indicating a possible cross-contamination. Moreover, we evaluated the accuracy of the proposed approach through the analysis of 27 hand-made mixtures with increasing amounts of a specific contaminant variety, allowing the estimation of the limit of detection of 5% (w/w).

CONCLUSION

We demonstrated the feasibility of the proposed method and its effectiveness in the detection of not declared varieties when these are present in a percentage equal to or higher than 5%. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The Application of High-Resolution Melting Analysis to trnL (UAA) Intron Allowed a Qualitative Identification of Apple Juice Adulterations

Food authenticity plays a pivotal role in the modern age since an increased consumers awareness has led them to pay more attention to food commodities. For this reason, it is important to have reliable and fast techniques able to detect possible adulterations in food, which affect qualitative and economic value. Therefore, the aim of this study was to detect possible adulterations in apple juice from others fruit species (i.e., pear, peach, and kiwi) combining DNA barcoding approach, using trnL (UAA) intron, with high resolution melting analysis (HRMA). A preliminary phylogenetic analysis, using sequences retrieved by the GenBank, confirmed the discriminatory power of trnL (UAA) intron among the four fruit species examined. Moreover, the sequencing of the trnL (UAA) fragments obtained from apple, pear, peach, and kiwi, demonstrated the suitability of an inner shorter sequence, P6 loop, to differentiate the considered species. The HRMA coupled with trnL (UAA) intron allowed discrimination among the four fruits but provided incomplete results for juices. Whereas the HRMA targeting the P6 loop amplicons confirmed the suitability of the technique to qualitatively distinguish fruit juices composed by the combination of apple/pear and apple/peach. However, the impossibility of discriminating apple/kiwi juices from the pure kiwi sample highlighted limitations, most likely related to the DNA extraction process. This hypothesis was further confirmed by analyzing DNA blends obtained by combining nucleic acids extracted from pure matrixes (i.e., apple and kiwi fruits). In this specific case, the application of HRMA allowed both qualitative and quantitative assessment of the samples.

Identification of the hazelnut cultivar in raw kernels and in semi-processed and processed products

The request for an efficient traceability system able to identify hazelnut cultivars along the entire processing chain is becoming a critical point for avoiding fraudulent practices and safeguarding the interests of growers, food processors and consumers. In this study, DNA was extracted from different hazelnut matrices, including plant material (leaf, kernel and kernel episperm), and processed foods (paste, grain, flour and different types of snacks containing hazelnuts). The efficiency of Simple Sequence Repeat (SSR) markers was tested to identify the hazelnut cultivar ‘Tonda Gentile’ in all the supply chain. The analysis at 10 SSR loci was able to verify the presence/absence of the alleles of a declared cultivar contained in these matrices. The SSR analysis of DNA from raw episperm offers the possibility of identifying the mother cultivar and is suggested as an effective way to discover frauds since DNA analysis can be performed on individual kernels. For food matrices containing hazelnuts, the presence of the mother cultivar’s DNA can be assessed based on the identification of its alleles in the sample, although the presence of multiple alleles from the pollenizers makes the interpretation of results more difficult.

cpSSR and High-Resolution Melting Analysis (HRM) for Pinus pseudostrobus Lindl. Variety Genotyping and Discrimination

The unambiguous identification of varieties within the Pseudostrobus complex is a key step to facilitate tree selection and monitoring in the wild as well as in plantations. Molecular tools provide a powerful approach for species delimitation; however, the use of DNA barcodes in this group has met limited success due to widespread haplotype sharing from lineage sorting, hybridization and introgression. Here, we evaluate the utility of real-time PCR coupled with high-resolution melting (HRM) to discriminate among Pinus pseudostrobus Lindl. var. pseudostrobus, apulcensis and oaxacana, from wild populations in central and southern Mexico, using chloroplast DNA sequence variants located within the clpP, ycf2, trnL(UAA)–trnT(UGU) and trnI(CAU)–trnF(GAA) loci. The markers ycf2/trnL(UAA)–trnT(UGU) produced clear melting patterns that separated the varieties pseudostrobus and oaxacana from type var. apulcensis, whereas clpP discriminated over 60% of var. oaxacana individuals. This assay underlines the usefulness of these less-used DNA regions as potential biological markers and exhibits the effect of geography on allele distribution and the likely presence of hybrids among the species and varieties.

Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

The olive fruit, a symbol of Mediterranean diets, is a rich source of antioxidants and oleic acid (55–83%). Olive genetic resources, including cultivated olives (cultivars), wild olives as well as related subspecies, are distributed widely across the Mediterranean region and other countries. Certain cultivars have a high commercial demand and economical value due to the differentiating organoleptic characteristics. This might result in economically motivated fraudulent practices and adulteration. Hence, tools to ensure the authenticity of constituent olive cultivars are crucial, and this can be achieved accurately through DNA-based methods. The present review outlines the applications of microsatellite markers, one of the most extensively used types of molecular markers in olive species, particularly referring to the use of these DNA-based markers in cataloging the vast olive germplasm, leading to identification and authentication of the cultivars. Emphasis has been given on the need to adopt a uniform platform where global molecular information pertaining to the details of available markers, cultivar-specific genotyping profiles (their synonyms or homonyms) and the comparative profiles of oil and reference leaf samples is accessible to researchers. The challenges of working with microsatellite markers and efforts underway, mainly advancements in genotyping methods which can be effectively incorporated in olive oil varietal testing, are also provided. Such efforts will pave the way for the development of more robust microsatellite marker-based olive agri-food authentication platforms.

Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review

In the last decades, the demand for molecular tools for authenticating and tracing agri-food products has significantly increased. Food safety and quality have gained an increased interest for consumers, producers, and retailers, therefore, the availability of analytical methods for the determination of food authenticity and the detection of major adulterations takes on a fundamental role. Among the different molecular approaches, some techniques such as the molecular markers-based methods are well established, while some innovative approaches such as isothermal amplification-based methods and DNA metabarcoding have only recently found application in the agri-food sector. In this review, we provide an overview of the most widely used molecular techniques for fresh and processed agri-food authentication and traceability, showing their recent advances and applications and discussing their main advantages and limitations. The application of these techniques to agri-food traceability and authentication can contribute a great deal to the reassurance of consumers in terms of transparency and food safety and may allow producers and retailers to adequately promote their products.

A review of fruit juice authenticity assessments: Targeted and untargeted analyses

Fruit juices are becoming more and more popular in the whole world. However, the increasing fruit juice fraud cases are undermining the healthy development of fruit juice industry. Fruit juice authenticity represents an important food quality and safety parameter. Many techniques have been applied in fruit juices authenticity assessment. The purpose of this review is to provide a research overview of the targeted and untargeted analyses of fruit authentication, and a method selection guide for fruit juice authenticity assessment. Targeted markers, such as stable isotopes, phenolics, carbohydrates, organic acids, volatile components, DNAs, amino acids and proteins, as well as carotenoids, will be discussed. And untargeted techniques, including liquid/gas chromatography-mass spectrometer, nuclear magnetic resonance, infrared spectroscopy, inductively-coupled plasma-mass spectrometry/optical emission spectrometer, fluorescence spectra, electronic sensors and others, will be reviewed. The emerging untargeted for novel targeted marker analysis will be also summarized.

Fruit quality trait discovery and metabolic profiling in sweet cherry genebank collection in Greece

The current study characterizes the physicochemical, sensory and bioactive compound traits of twenty-two sweet cherry accessions, namely breeding lines, landraces and modern cultivars, embodying the majority of Greek germplasm. The evaluated accessions differ in several quality traits including colour parameters and textural properties as well as sensory attributes, such as taste intensity and overall acceptance. Significant differences in primary metabolites, including fructose, glucose, sorbitol, malic acid were recorded among tested accessions. All genotypes were rich in polyphenols, primarily in quercetin-3,4-O-diglucoside, esculetin, rutin and neochlorogenic acid. An anthocyanins-related discrimination among accessions was also obtained based on cyanidin-3-O-rutinoside and peonidin glycosides content. Overall, the cultivars 'Tsolakeika' and 'Bakirtzeika' exhibited the higher consumer acceptance while the cultivars 'Vasiliadi' and 'Tragana Edessis-Naousis' and especially the breeding line 'TxAg33' contained high polyphenol levels. These results represent a valuable resource for future breeding efforts for sweet cherry cultivars with improved nutritional quality traits.

High Resolution Melting (HRM) Genotyping in the Genus Origanum: Molecular Identification and Discrimination for Authentication Purposes

Origanum L. (Lamiaceae) is an important genus of medicinal and aromatic plants used since ancient times as culinary herbs and remedies in traditional medicine. Although it is a relatively small genus, intra-generic species delineation, as well as its inter-generic relationships within tribe Mentheae, are still poorly understood. High resolution melting (HRM) analysis, coupled with microsatellite markers (SSRs), could facilitate the molecular identification and characterization of certain genotypes more efficiently and relatively faster when compared to other analytical methods. In this study, 38 Origanum samples corresponding to six Origanum taxa (O. dictamnus, O. majorana, O. onites, O. scabrum, O. sipyleum, and O. vulgare subsp. hirtum) were analyzed, using six microsatellite loci. Our goal was to molecularly identify and discriminate among the selected samples and to evaluate the ability of the HRM technique as an analytical tool for the discrimination of Origanum species from Greece. The temperature-shifted melting curves produced by the HRM analysis, resulted in 98 unique HRM profiles, which enabled the discrimination of the Origanum genotypes studied. According to the similarity dendrogram based on the HRM profiles, six unique clusters were formed, each one corresponding to a single taxon. In conclusion, HRM genotyping provided a fast, cost-effective method, well suited for the molecular characterization and identification of Origanum taxa and for the authentication of the original genetic material.

Analysis of Microsatellites (SSRs) in Processed Olives as a Means of Cultivar Traceability and Authentication

Select cultivars of table olives have more desirable traits and a higher economic value. There are suspected issues with cultivar mislabeling and traceability in the supply chain. Here, we describe a method to identify cultivars by genotyping of processed olives. DNA was extracted from leaves and California-style olives of seven commonly packed cultivars. Processed olive fruits yielded relatively low DNA concentrations (0.04-0.86 μg/g), and extracts had more impurities compared with leaves. From 15 candidate SSRs, five markers showing the highest number of unique allele combinations and discriminatory power were selected. These SSRs were successfully amplified and analyzed in all cultivars of olives except one. When directly comparing any two cultivars, different allele combinations were typically present for at least four of the five SSRs. Microsatellite analysis shows potential as a simple yet robust diagnostic tool. The method can be expanded to include other cultivars, styles of table olives, and potentially other processed plant-based foods.

GLADS: A gel-less approach for detection of STMS markers in wheat and rice

Sequence tagged microsatellite site (STMS) are useful PCR based DNA markers. Wide genome coverage, high polymorphic index and co-dominant nature make STMS a preferred choice for marker assisted selection (MAS), genetic diversity analysis, linkage mapping, seed genetic purity analysis etc. Routine STMS analysis involving low-throughput, laborious and time-consuming polyacrylamide/agarose gels often limit their full utility in crop breeding experiments that involve large populations. Therefore, convenient, gel-less marker detection methods are highly desirable for STMS markers. The present study demonstrated the utility of SYBR Green dye based melt-profiling as a simple and convenient gel-less approach for detection of STMS markers (referred to as GLADS) in bread wheat and rice. The method involves use of SYBR Green dye during PCR amplification (or post-PCR) of STMS markers followed by generation of a melt-profile using controlled temperature ramp rate. The STMS amplicons yielded characteristic melt-profiles with differences in melting temperature (Tm) and profile shape. These characteristic features enabled melt-profile based detection and differentiation of STMS markers/alleles in a gel-less manner. The melt-profile approach allowed assessment of the specificity of the PCR assay unlike the end-point signal detection assays. The method also allowed multiplexing of two STMS markers with non-overlapping melt-profiles. In principle, the approach can be effectively used in any crop for STMS marker analysis. This SYBR Green melt-profiling based GLADS approach offers a convenient, low-cost (20-51%) and time-saving alternative for STMS marker detection that can reduce dependence on gel-based detection, and exposure to toxic chemicals.

Microsatellite High-Resolution Melting (SSR-HRM) to Track Olive Genotypes: From Field to Olive Oil

The need to support food labelling has driven to the development of PCR-based techniques suitable for food analysis. DNA-based markers have been successfully employed for varietal tracing in Protected Designation of Origin (PDO) olive oils. In this study, we report a fast, sensitive, and easy-to-use strategy for PDO olive varietal identification. To achieve this aim four different DNA extraction methods were tested and compared, based on initial volume, extraction time, the gDNA concentration, and quality ratios. The optimized DNA extraction protocol from extra virgin olive oils, based on CTAB-hexane-chloroform extraction, proved to be the most effective. High-resolution melting (HRM) DNA assay was developed based on nuclear microsatellites (gSSR) and plastid DNA (cpDNA) aiming an accurate identification of the olive varieties present in the olive oil samples. After PCR reproducibility evaluation, six molecular markers: three SSRs and three cpDNA loci were chosen based on their discrimination power. The SSR-HRM strategy assays were designed to target UDO99-011, UDO99-039, UDO99-024, and ssrOeUA-DCA16 loci. All SSR-PCR products generated from these primers were analyzed by capillary electrophoresis (CE) for HRM data validation. The SSR coupled with HRM melting curve analysis generated 14 HRM profiles sufficient to genotype all varieties, highlighting their potential use for varietal discrimination. The locus ssrOeUA-DCA16 generated a specific melting curve that allow a high-throughput discrimination of the Picual and Cobrançosa varieties in olive oil samples. Further, the UDO99-024 was also tested by SSR-HRM assay in commercial olive oil samples with promising results. Considering time, cost, and performance SSR-HRM proved to be a reliable method suitable for varietal tracing of olive oils. PRACTICAL APPLICATION: Olive oil authenticity is a form of protecting producers and consumers against fraudulent practices. Herein, we present a DNA barcode suitable for the identification of olive varieties, allowing an accurate identification of the olive varieties in olive oil samples using SSR-HRM assay. Its applicability in commercial olive oil samples is viable. This methodology can be used as a tool for Extra Virgin Olive Oil (EVOO) adulterations detection.

A new high-resolution melting assay for genotyping Alternaria species causing citrus brown spot

BACKGROUND

Alternaria brown spot is one of the most important diseases of tangerines and their hybrids worldwide. To set up effective control strategy, the accurate detection and identification of the species responsible for the diseases is crucial. However, characterization based on morphology and/or multilocus genetic approaches is time consuming, requires great expertise and sometimes is not conclusive. Therefore, the set-up of a rapid and efficient DNA-based assay might be of paramount importance. High-resolution melting (HRM) analysis represents an interesting tool for the uncovering of nucleotide variations as small as one base difference and, as such, relevant to species characterization.

RESULTS

In the present investigation, an HRM assay based on the Alternaria barcoding region OPA1-3 was set up. Specimen strains of the main citrus-associated Alternaria species and morphotypes generated distinct and normalized profiles, allowing their differentiation when HRM-tested. Moreover, when the assay was used to screen an Alternaria collection from citrus fruit and leaves, it distributed the 180 isolates in three independent clusters, readily and consistently resolved. Isolates were identified as belonging to the species Alternaria alternata and the species complex A. arborescens. Within A. alternata, the morphotypes alternata (77% of the collection) and limoniasperae (17% of the collection) were present.

CONCLUSIONS

Although further validation experiments will be performed to optimize the assay for a diagnostic use, this HRM approach might represent a rapid, sensitive and specific method for the detection and identification of Alternaria spp. responsible for citrus brown spot disease. © 2018 Society of Chemical Industry.

Haplotype analysis of the germacrene A synthase gene and association with cynaropicrin content and biological activities in Cynara cardunculus

Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropicrin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from different origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities. Using high-resolution melting, nine haplotypes were identified. The putative impact of the identified allelic variants in GAS protein was evaluated by bioinformatic tools and polymorphisms that putatively lead to protein conformational changes were described. Additionally, cynaropicrin and main pentacyclic triterpenes contents, and antithrombin, antimicrobial and antiproliferative activities were also determined in C. cardunculus leaf lipophilic-derived extracts. In this work we identified allelic variants with putative impact on GAS protein, which are significantly associated with cynaropicrin content and antiproliferative activity. The results obtained suggest that the identified polymorphisms should be explored as putative genetic markers correlated with biological properties in Cynara cardunculus.

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N₅₀ length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers

The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits.

ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger

Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use.

Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

BACKGROUND

Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities.

RESULTS

In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3'-hydroxylase (C3'H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3'H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3'H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms.

CONCLUSION

In this work we identified allelic variants with putative impact on C3'H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.

High-Resolution DNA Melting Analysis in Plant Research

Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.

Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid

Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.

Traceability of PDO Olive Oil “Terra di Bari” Using High Resolution Melting

The aim of the research was to verify the applicability of microsatellite (SSR) markers in High Resolution Melting (HRM) analysis for the identification of the olive cultivars used in the “Terra di Bari” PDO extra virgin olive oil. A panel of nine cultivars, widespread in Apulia region, was tested with seventeen SSR primer pairs and the PCR products were at first analysed with a Genetic Analyzer automatic sequencer. An identification key was obtained for the nine cultivars, which showed an unambiguous discrimination among the varieties constituting the “Terra di Bari” PDO extra virgin olive oil: Cima di Bitonto, Coratina, and Ogliarola. Subsequently, an SSR based method was set up with the DCA18 marker, coupled with HRM analysis for the distinction of the Terra di Bari olive oil from non-Terra di Bari olive oil using different mixtures. Thus, this analysis enabled the distinction and identification of the PDO mixtures. Hence, this assay provided a flexible, cost-effective, and closed-tube microsatellite genotyping method, well suited to varietal identification and authentication analysis in olive oil.

De novo transcriptome assembly and the identification of gene-associated single-nucleotide polymorphism markers in Asian and American ginseng roots

We performed de novo transcriptome sequencing for Panax ginseng and Panax quinquefolius accessions using the 454 GS FLX Titanium System and discovered annotation-based genome-wide single-nucleotide polymorphism (SNPs) using next-generation ginseng transcriptome data without reference genome sequence. The comprehensive transcriptome characterization with the mature roots of four ginseng accessions generated 297,170 reads for 'Cheonryang' cultivar, 305,673 reads for 'Yunpoong' cultivar, 311,861 reads for the G03080 breeding line, and 308,313 reads for P. quinquefolius. In transcriptome assembly, the lengths of the sample read were 156.42 Mb for 'Cheonryang', 161.95 Mb for 'Yunpoong', 165.07 Mb for G03080 breeding line, and 166.48 Mb for P. quinquefolius. A total of 97 primer pairs were designed with the homozygous SNP presented in all four accessions. SNP genotyping using high-resolution melting (HRM) analysis was performed to validate the putative SNP markers of 97 primer pairs. Out of the 73 primer pairs, 73 primer pairs amplified the target sequence and 34 primer pairs showed polymorphic melting curves in samples from 11 P. ginseng cultivars and one P. quinquefolius accession. Among the 34 polymorphic HRM-SNP primers, four primers were useful to distinguish ginseng cultivars. In the present study, we demonstrated that de novo transcriptome assembly and mapping analyses are useful in providing four HRM-SNP primer pairs that reliably show a high degree of polymorphism among ginseng cultivars.

DNA barcode ITS2 coupled with high resolution melting (HRM) analysis for taxonomic identification of Sideritis species growing in Greece

Identification of genotypes in Sideritis is complicated owing to the morphological similarity and common occurrence of natural hybridisation within Sideritis species. Species- and genotype-specific DNA markers are very useful for plant identification, breeding and preservation programs. Herein, a real-time polymerase chain reaction (PCR) of ITS2 barcode region coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on seven Sideritis species growing in Greece. The HRM assay developed in this study is a rapid and straightforward method for the identification and discrimination of the investigated Sideritis species. This assay is simple compared to other genotyping methods as it does not require DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of Sideritis species.

High resolution melting (HRM) analysis of DNA--its role and potential in food analysis

DNA based methods play an increasing role in food safety control and food adulteration detection. Recent papers show that high resolution melting (HRM) analysis is an interesting approach. It involves amplification of the target of interest in the presence of a saturation dye by the polymerase chain reaction (PCR) and subsequent melting of the amplicons by gradually increasing the temperature. Since the melting profile depends on the GC content, length, sequence and strand complementarity of the product, HRM analysis is highly suitable for the detection of single-base variants and small insertions or deletions. The review gives an introduction into HRM analysis, covers important aspects in the development of an HRM analysis method and describes how HRM data are analysed and interpreted. Then we discuss the potential of HRM analysis based methods in food analysis, i.e. for the identification of closely related species and cultivars and the identification of pathogenic microorganisms.

Microsatellites: evolution and contribution

Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed.

Barcode DNA high-resolution melting (Bar-HRM) analysis as a novel close-tubed and accurate tool for olive oil forensic use

BACKGROUND

The adulteration of high-priced olive oil with low-cost oils and the fraudulent labelling of oil products make the identification and traceability of vegetable oil species in the food chain very important. This paper describes a high-resolution melting analysis-based method using chloroplast barcoding regions as target (Bar-HRM) to obtain barcoding information for the major vegetable oil species and to quantitatively identify the botanical origin of plant oils. The detection of adulteration of olive oil with canola oil was used as a case study.

RESULTS

The proposed method was capable of distinguishing among different vegetable oil species and detecting a level of 1% (w/w) of canola oil in olive oil.

CONCLUSION

Bar-HRM analysis is a more accurate, faster and less costly alternative method to authenticate vegetable oils, including olive oil, and to detect mixtures of oils.