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Chang L, Liang J, Cai X, Zhang L, Li Y, Wu J, Wang X. Development of self-compatible Chinese cabbage lines of Chiifu through marker-assisted selection. FRONTIERS IN PLANT SCIENCE 2024; 15:1397018. [PMID: 38872891 PMCID: PMC11169807 DOI: 10.3389/fpls.2024.1397018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
The continuously refined genome assembly of the Chinese cabbage accession Chiifu is widely recognized as the reference for Brassica rapa. However, the high self-incompatibility of Chiifu limits its broader utilization. In this study, we report the development of self-compatible Chiifu lines through a meticulous marker-assisted selection (MAS) strategy, involving the substitution of the Chiifu allele of MLPK (M-locus protein kinase) with that from the self-compatible Yellow Sarson (YS). A YS-based marker (SC-MLPK) was employed to screen 841 B. rapa accessions, confirming that all eight accessions with the mlpk/mlpk (mm) genotype exhibited self-compatibility. Additionally, we designed 131 High-Resolution Melting (HRM) markers evenly distributed across the B. rapa genome as genomic background selection (GBS) markers to facilitate the introgression of self-compatibility from YS into Chiifu along with SC-MLPK. Genome background screening revealed that the BC3S1 population had a proportion of the recurrent parent genome (PR) ranging from 93.9% to 98.5%. From this population, we identified self-compatible individuals exhibiting a high number of pollen tubes penetrating stigmas (NPT) (>25) and a maximum compatibility index (CI) value of 7.5. Furthermore, we selected two individuals demonstrating significant similarity to Chiifu in both genetic background and morphological appearance, alongside self-compatibility. These selected individuals were self-pollinated to generate two novel lines designated as SC-Chiifu Lines. The development of these self-compatible Chiifu lines, together with the SC-MLPK marker and the set of HRM markers, represents valuable tools for B. rapa genetics and breeding.
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Affiliation(s)
| | | | | | | | | | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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2
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Alderotti F, Sillo F, Brilli L, Bussotti F, Centritto M, Ferrini F, Gori A, Inghes R, Pasquini D, Pollastrini M, Saurer M, Cherubini P, Balestrini R, Brunetti C. Quercus ilex L. dieback is genetically determined: Evidence provided by dendrochronology, δ 13C and SSR genotyping. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166809. [PMID: 37690750 DOI: 10.1016/j.scitotenv.2023.166809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/20/2023] [Accepted: 09/02/2023] [Indexed: 09/12/2023]
Abstract
Quercus ilex L. dieback has been reported in several Mediterranean forests, revealing different degree of crown damages even in close sites, as observed in two Q. ilex forest stands in southern Tuscany (IT). In this work, we applied a novel approach combining dendrochronological, tree-ring δ13C and genetic analysis to test the hypothesis that different damage levels observed in a declining (D) and non-declining (ND) Q. ilex stands are connected to population features linked to distinct response to drought. Furthermore, we investigated the impact of two major drought events (2012 and 2017), that occurred in the last fifteen years in central Italy, on Q. ilex growth and intrinsic water use efficiency (WUEi). Overall, Q. ilex showed slightly different ring-width patterns between the two stands, suggesting a lower responsiveness to seasonal climatic variations for trees at D stand, while Q. ilex at ND stand showed changes in the relationship between climatic parameters and growth across time. The strong divergence in δ13C signals between the two stands suggested a more conservative use of water for Q. ilex at ND compared to D stand that may be genetically driven. Q. ilex at ND resulted more resilient to drought compared to trees at D, probably thanks to its safer water strategy. Genotyping analysis based on simple-sequence repeat (SSR) markers revealed the presence of different Q. ilex populations at D and ND stands. Our study shows intraspecific variations in drought response among trees grown in close. In addition, it highlights the potential of combining tree-ring δ13C data with SSR genotyping for the selection of seed-bearing genotypes aimed to preserve Mediterranean holm oak ecosystem and improve its forest management.
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Affiliation(s)
- Francesca Alderotti
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy; National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Fabiano Sillo
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Lorenzo Brilli
- CNR-IBE, National Research Council of Italy (CNR), Institute for the BioEconomy, Via Caproni 8, 50145 Firenze, Italy
| | - Filippo Bussotti
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy
| | - Mauro Centritto
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Francesco Ferrini
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy; National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy; National Biodiversity Future Center (www.nfbc.it), Italy
| | - Antonella Gori
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy; National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Roberto Inghes
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Dalila Pasquini
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy
| | - Martina Pollastrini
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy; National Biodiversity Future Center (www.nfbc.it), Italy
| | - Matthias Saurer
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Paolo Cherubini
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland; University of British Columbia, Department of Forest and Conservation Sciences, Vancouver, BC, Canada
| | - Raffaella Balestrini
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy
| | - Cecilia Brunetti
- University of Florence, Department of Agriculture, Food, Environment and Forestry, Viale delle idee 30, 50019 Sesto Fiorentino, Piazzale delle Cascine 28, 50144 Florence, Italy; National Research Council of Italy (CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy; Strada delle Cacce 73, 10135, Torino, Italy.
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3
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Xu X, Wang N, Feng L, Wang J. Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing Rosa rugosa via High-Resolution Melting (HRM) Analysis. Biomolecules 2023; 13:1468. [PMID: 37892150 PMCID: PMC10605111 DOI: 10.3390/biom13101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Oil-bearing Rosa rugosa are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of R. rugosa. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of R. rugosa and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3-9 genotypes among the 19 R. rugosa cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield R. rugosa and be helpful for the selection and breeding of oil-bearing roses.
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Affiliation(s)
| | | | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
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Wanere SS, Phad AP, Jagtap RK, Rawal SK, Pyati PS, Lomate PR. Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries. Anal Biochem 2023; 676:115245. [PMID: 37429485 DOI: 10.1016/j.ab.2023.115245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Genetic purity of seeds is one of the critical aspects in the seed industry. Molecular seed testing laboratories are utilizing PCR based diagnostic tools for genetic purity analysis. High quality DNA is an essential prerequisite for such analyses. Here, we demonstrate a robust and inexpensive DNA extraction method to isolate genomic DNA from variety of crops. Current method (M2) was compared with four commonly used DNA isolation methods for PCR-based genetic characterization and High Resolution Melt (HRM) based hybridity analysis of cotton, okra, tomato and maize using SSR markers. DNA extracted through current method showed excellent yield and quality as compared to other methods. High quality, PCR ready DNA was isolated within 30-50 min and displayed best results for genetic purity analysis using HRM. In contrast, several genomic DNA samples extracted using other methods were found unsuitable for HRM analysis. Our method can be a perfect choice in seed industry, where thousands of samples are processed every day. Notably, using our method single technician can extract DNA from 96 leaf samples within 30-50 min, at a cost of only $0.11/sample. Overall, current DNA extraction method is a reliable and cost-effective solution for large-scale genotyping experiments in the agricultural industry.
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Affiliation(s)
- Shyamkumar S Wanere
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Archana P Phad
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Rameshwar K Jagtap
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Shuban K Rawal
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Prashant S Pyati
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
| | - Purushottam R Lomate
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
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5
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Torres A, Pauli C, Givens R, Argyris J, Allen K, Monfort A, Gaudino RJ. High-throughput methods to identify male Cannabis sativa using various genotyping methods. J Cannabis Res 2022; 4:57. [PMID: 36324130 PMCID: PMC9628020 DOI: 10.1186/s42238-022-00164-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Background Cannabis sativa is a primarily dioecious angiosperm that exhibits sexual developmental plasticity. Developmental genes for staminate male flowers have yet to be elucidated; however, there are regions of male-associated DNA from Cannabis (MADC) that correlate with the formation of pollen producing staminate flowers. MADC2 is an example of a PCR-based genetic marker that has been shown to produce a 390-bp amplicon that correlates with the expression of male phenotypes. We demonstrate applications of a cost-effective high-throughput male genotyping assay and other genotyping applications of male identification in Cannabis sativa. Methods In this study, we assessed data from 8200 leaf samples analyzed for real-time quantitative polymerase chain reaction (qPCR) detection of MADC2 in a commercial testing application offered through Steep Hill Laboratories. Through validation, collaborative research projects, and follow-up retest analysis, we observed a > 98.5% accuracy of detection of MADC2 by qPCR. We also carried out assay development for high-resolution melting analysis (HRM), loop-mediated isothermal amplification (LAMP), and TwistDx recombinase amplification (RPA) assays using MADC2 for male identification. Results We demonstrate a robust high-throughput duplex TaqMan qPCR assay for identification of male-specific genomic signatures using a novel MADC2 qPCR probe. The qPCR cycle quotient (Cq) value representative of MADC2 detection in 3156 males and the detection of tissue control cannabinoid synthesis for 8200 samples and the absence of MADC2 detection in 5047 non-males demonstrate a robust high-throughput real-time genotyping assay for Cannabis. Furthermore, we also demonstrated the viability of using nearby regions to MADC2 with novel primers as alternative assays. Finally, we also show proof of concept of several additional commercially viable sex determination methodologies for Cannabis sativa. Discussion In industrial applications, males are desirable for their more rapid growth and higher quality fiber quality, as well as their ability to pollinate female plants and produce grain. In medicinal applications, female cultivars are more desirable for their ability to produce large amounts of secondary metabolites, specifically the cannabinoids, terpenes, and flavonoids that have various medicinal and recreational properties. In previous studies, traditional PCR and non-high-throughput methods have been reported for the detection of male cannabis, and in our study, we present multiple methodologies that can be carried out in high-throughput commercial cannabis testing. Conclusion With these markers developed for high-throughput testing assays, the Cannabis industry will be able to easily screen and select for the desired sex of a given cultivar depending on the application. Supplementary Information The online version contains supplementary material available at 10.1186/s42238-022-00164-7.
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Affiliation(s)
| | | | | | - Jason Argyris
- Centre for Agriculture and Genomics Research, Barcelona, Spain
| | | | - Amparo Monfort
- Centre for Agriculture and Genomics Research, Barcelona, Spain
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6
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Pasqualetto G, Palmieri L, Martens S, Bus VGM, Chagné D, Wiedow C, Malnoy MA, Gardiner SE. Molecular characterization of intergeneric hybrids between Malus and Pyrus. HORTICULTURE RESEARCH 2022; 10:uhac239. [PMID: 36643755 PMCID: PMC9832871 DOI: 10.1093/hr/uhac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Apple (Malus) and pear (Pyrus) are economically important fruit crops well known for their unique textures, flavours, and nutritional qualities. Both genera are characterised by a distinct pattern of secondary metabolites, which directly affect not only resistance to certain diseases, but also have significant impacts on the flavour and nutritional value of the fruit. The identical chromosome numbers, similar genome size, and their recent divergence date, together with DNA markers have shown that apple and pear genomes are highly co-linear. This study utilized comparative genomic approaches, including simple sequence repeats, high resolution single nucleotide polymorphism melting analysis, and single nucleotide polymorphism chip analysis to identify genetic differences among hybrids of Malus and Pyrus, and F2 offspring. This research has demonstrated and validated that these three marker types, along with metabolomics analysis are very powerful tools to detect and confirm hybridity of progeny derived from crosses between apple and pear in both cross directions. Furthermore, this work analysed the genus-specific metabolite patterns and the resistance to fire blight (Erwinia amylovora) in progeny. The findings of this work will enhance and accelerate the breeding of novel tree fruit crops that benefit producers and consumers, by enabling marker assisted selection of desired traits introgressed between pear and apple.
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Affiliation(s)
- Giulia Pasqualetto
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, UD 33100, Italy
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Luisa Palmieri
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Vincent G M Bus
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - David Chagné
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Claudia Wiedow
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Mickael A Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
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Ismail A, Gajjar P, Park M, Mahboob A, Tsolova V, Subramanian J, Darwish AG, El-Sharkawy I. A recessive mutation in muscadine grapes causes berry color-loss without influencing anthocyanin pathway. Commun Biol 2022; 5:1012. [PMID: 36153380 PMCID: PMC9509324 DOI: 10.1038/s42003-022-04001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Anthocyanins, a major class of flavonoids, are important pigments of grape berries. Despite the recent discovery of the genetic cause underlying the loss of color, the metabolomic and molecular responses are unknown. Anthocyanin quantification among diverse berry color muscadines suggests that all genotypes could produce adequate anthocyanin quantities, irrespective of berry color. Transcriptome profiling of contrasting color muscadine genotypes proposes a potential deficiency that occurs within the anthocyanin transport and/or degradation mechanisms and might cause unpigmented berries. Genome-wide association studies highlighted a region on chromosome-4, comprising several genes encoding glutathione S-transferases involved in anthocyanin transport. Sequence comparison among genotypes reveals the presence of two GST4b alleles that differ by substituting the conserved amino acid residue Pro171-to-Leu. Molecular dynamics simulations demonstrate that GST4b2–Leu171 encodes an inactive protein due to modifications within the H-binding site. Population genotyping suggests the recessive inheritance of the unpigmented trait with a GST4b2/2 homozygous. A model defining colorless muscadines’ response to the mutation stimulus, avoiding the impact of trapped anthocyanins within the cytoplasm is established. Transcriptome profiling and mutational analysis suggest a potential deficiency in anthocyanin transport by glutathione S-transferases and/or degradation mechanisms that might cause unpigmented berries.
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Alirezaei M, Mosawi SH, Afgar A, Zarean M, Movahhed TK, Abbasi V, Fotouhi-Ardakani R. Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Sci Rep 2022; 12:13943. [PMID: 35977949 PMCID: PMC9382607 DOI: 10.1038/s41598-022-14730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
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Affiliation(s)
- Melika Alirezaei
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | | | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Komeili Movahhed
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Vajiheh Abbasi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran. .,Department of Medical Biotechnology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
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9
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Abstract
Genome engineering technologies enable targeted mutations to be induced at almost any location in plant genomes. In particular, Cas9 nucleases use easily recoded RNA guides to target user-defined sequences and generate double-stranded breaks (DSB) that are then repaired by the cell's endogenous repair mechanisms. Incorrect repair results in mutations at the target. When the targets are in coding sequences, this often results in loss-of-function mutations. In this chapter, we describe a method to rapidly design and assemble RNA-guided Cas9 constructs for plants and test their ability to induce mutations at their intended targets in rapid assays using both Agrobacterium-mediated transient expression and PEG-mediated DNA delivery to protoplasts, the latter of which can be adapted to a wide range of plant species. We describe a PCR-based method for detecting mutagenesis and outline the steps required to segregate the Cas9 transgene from the targeted mutation to enable the production of transgene-free mutated plants. These techniques are amenable to a range of plant species and should accelerate the application of Cas-9-mediated genome engineering for basic plant science as well as crop development.
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10
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Yadav S, Carvalho J, Trujillo I, Prado M. Microsatellite Markers in Olives ( Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies. Foods 2021; 10:foods10081907. [PMID: 34441688 PMCID: PMC8394707 DOI: 10.3390/foods10081907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Shambhavi Yadav
- Genetics and Tree Improvement Division, Forest Research Institute, P.O. New Forest, Dehradun 248001, India
- Correspondence: (S.Y.); (I.T.)
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
- Department of Analytical Chemistry, Nutrition and Food Science, Campus Vida, College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Isabel Trujillo
- Excellence Unit of Maria de Maeztu, Department of Agronomy, Rabanales Campus, International Campus of Excellence on Agrofood (ceiA3), University of Córdoba, 14014 Córdoba, Spain
- Correspondence: (S.Y.); (I.T.)
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
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Muñoz-Espinoza C, Di Genova A, Sánchez A, Correa J, Espinoza A, Meneses C, Maass A, Orellana A, Hinrichsen P. Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches. BMC PLANT BIOLOGY 2020; 20:365. [PMID: 32746778 PMCID: PMC7397606 DOI: 10.1186/s12870-020-02564-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/21/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
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Affiliation(s)
- Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Alex Di Genova
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - Alicia Sánchez
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - José Correa
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Alonso Espinoza
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Alejandro Maass
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
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12
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Chedid E, Rizou M, Kalaitzis P. Application of high resolution melting combined with DNA-based markers for quantitative analysis of olive oil authenticity and adulteration. Food Chem X 2020; 6:100082. [PMID: 32154510 PMCID: PMC7058896 DOI: 10.1016/j.fochx.2020.100082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
A plethora of biotechnological methodologies is used to authenticate quality olive oils. Among the DNA-based approaches, SNPs and SSRs combined with high resolution melting (HRM) provide certain advantages such as speed, simplicity and reliability. SNP-HRM and SSR-HRM were used for the authentication of monovarietal olive oils as well as the quantification of varietal composition in olive oil DNA admixtures and olive oil blends of two different cultivars. The SSR-HRM was more efficient in distinguishing monovarietal olive oils while the SNP-HRM assay was more reliable in discriminating olive oil blends. HRM was also used for the detection of adulteration of olive oil with oils of different plant origin by using plastid trnL indels and SNPs. The trnL-indels-HRM showed higher discrimination power than the trnL-SNP-HRM in determining adulteration in olive oil. These results indicate that traceability of adulteration might be more reliable than authentication of the varietal origin in olive oil blends.
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Affiliation(s)
| | | | - Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania, Crete, Greece
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13
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Galuszynski NC, Potts AJ. Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush). PeerJ 2020; 8:e9187. [PMID: 32461839 PMCID: PMC7233275 DOI: 10.7717/peerj.9187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses). Conclusions After screening for regions with high HRM clustering specificity-akin to the screening process associated with most PCR based markers-the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.
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Affiliation(s)
- Nicholas C Galuszynski
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Alastair J Potts
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
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14
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Papaioannou C, Zeliou K, Trigas P, Papasotiropoulos V. High Resolution Melting (HRM) Genotyping in the Genus Origanum: Molecular Identification and Discrimination for Authentication Purposes. Biochem Genet 2020; 58:725-737. [PMID: 32394225 DOI: 10.1007/s10528-020-09970-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/04/2020] [Indexed: 12/25/2022]
Abstract
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.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Agriculture, University of Patras, Theodoropoulou Str, 27200, Amaliada, Greece.,Laboratory of Genetics, Department of Biology, University of Patras, 26504, Patras, Greece
| | - Konstantina Zeliou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Panayiotis Trigas
- Laboratory of Systematic Botany, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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15
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Li J, Demesyeux L, Brym M, Chambers AH. Development of species-specific molecular markers in Vanilla for seedling selection of hybrids. Mol Biol Rep 2020; 47:1905-1920. [PMID: 32026319 DOI: 10.1007/s11033-020-05287-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/27/2020] [Indexed: 11/29/2022]
Abstract
Vanilla planifolia is the primary botanical source of vanilla extract used globally in various foods and beverages. V. planifolia has a global distribution based on a few foundational clones and therefore has limited genetic diversity. Many Vanilla species easily hybridize with V. planifolia and could be a source of valuable genetic traits like increased vanillin content, disease resistance, or early flowering. While breeding Vanilla hybrids may improve plant performance, basic molecular tools for this species are lacking. DNA-based molecular markers are the most efficient method to validate hybrid progeny, detect hybrids in commercial plantings, and identify unknown accessions. This study used publicly available sequence data to develop species-specific, qRT-PCR-based molecular markers for Vanilla. Over 580,000 assembled sequence fragments were filtered for species specificity and twenty-two targets were selected for qRT-PCR screening. Ten targets differentially amplified among V. planifolia, V. pompona, V. phaeantha, and V. palmarum with ΔCT values as high as 17.58 between species. The ten targets were used to validate the parentage of hybrid progeny from controlled crosses with most hybrid progeny showing amplification patterns similar to both parents. The ten targets were also used to screen sixteen Vanilla species for specificity, and supported species assignments for unknown accessions including the detection of putative hybrids. This is the first report using species-specific, qRT-PCR-based molecular markers in Vanilla. These markers are inexpensive, simple to develop, and can rapidly screen large populations. These methods will enable the further development of species-specific molecular markers when creating Vanilla interspecific hybrid populations.
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Affiliation(s)
- Juan Li
- Department of Horticulture, Zhongkai University of Agriculture and Engineering, 501 Zhongkai Rd., Guangzhou, 510225, Guangdong, China.,Horticultural Sciences Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL, 33031, USA
| | - Lynhe Demesyeux
- Horticultural Sciences Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL, 33031, USA
| | - Maria Brym
- Horticultural Sciences Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL, 33031, USA
| | - Alan H Chambers
- Horticultural Sciences Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL, 33031, USA.
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16
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Rapid detection and genotyping of ALK fusion variants by adapter multiplex PCR and high-resolution melting analysis. J Transl Med 2020; 100:110-119. [PMID: 31641223 DOI: 10.1038/s41374-019-0330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/08/2019] [Accepted: 09/07/2019] [Indexed: 11/08/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusion is a promising predictive biomarker of ALK-tyrosine kinase inhibitor (ALK-TKI) treatment. Furthermore, different fusion variants correlate to different ALK-TKIs responses. Although variant identification assists in treatment direction, most ALK detection assays do not genotype different fusion variants. We developed a high-resolution melting (HRM) assay to rapidly detect ALK fusions and automatically distinguish at least 20 fusion variants in one tube. Adapter multiplex PCR was designed to amplify ALK fusion variants and the reference gene GAPDH. After HRM, negative derivative curves showed a low temperature GAPDH peak, and if an ALK fusion was present, a high temperature peak from the ALK segment and variably a middle temperature part associated with the fusion partner. Selected regions of the second derivative curves were analyzed to extract features (∆Tm, PTS/ITS, H1/H2) that define two curve types (monotonic and non-monotonic). Synthetic samples of 20 ALK fusion variants were used to train a quadratic discriminate analysis model, and the accuracy was 97.06% (66/68) and 85.71% (144/162) for monotonic and non-monotonic variants, respectively. The limit of detection of the assay was 1%. The analytical sensitivity of genotyping was 1 and 5% for monotonic and non-monotonic variants, respectively. In a blinded study, we detected ALK fusion from formalin-fixed paraffin-embedded lung cancer samples with a 100% 47) and genotyping /47) and genotyping (7/7). Multiplex adapter HRM is a simple, fast, and sensitive way of ALK fusion detection and genotyping. Automatic genotyping with parameters extracted from second derivative curves is a promising method that may be applicable to other types of gene variants detected by HRM.
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17
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Chatzidimopoulos M, Ganopoulos I, Moraitou-Daponta E, Lioliopoulou F, Ntantali O, Panagiotaki P, Vellios EK. High-Resolution Melting (HRM) Analysis Reveals Genotypic Differentiation of Venturia inaequalis Populations in Greece. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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18
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Vishwakarma G, Sanyal RP, Saini A, Sahu PK, Singh Patel RR, Sharma D, Tiwari R, Das BK. GLADS: A gel-less approach for detection of STMS markers in wheat and rice. PLoS One 2019; 14:e0224572. [PMID: 31689318 PMCID: PMC6830750 DOI: 10.1371/journal.pone.0224572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
| | - Ravi Prakash Sanyal
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Ajay Saini
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ravi Raj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ratan Tiwari
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
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19
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Apinjoh TO, Ouattara A, Titanji VPK, Djimde A, Amambua-Ngwa A. Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa? Malar J 2019; 18:217. [PMID: 31242921 PMCID: PMC6595576 DOI: 10.1186/s12936-019-2844-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The intensification of malaria control interventions has resulted in its global decline, but it remains a significant public health burden especially in sub-Saharan Africa (sSA). Knowledge on the parasite diversity, its transmission dynamics, mechanisms of adaptation to environmental and interventional pressures could help refine or develop new control and elimination strategies. Critical to this is the accurate assessment of the parasite’s genetic diversity and monitoring of genetic markers of anti-malarial resistance across all susceptible populations. Such wide molecular surveillance will require selected tools and approaches from a variety of ever evolving advancements in technology and the changing epidemiology of malaria. The choice of an effective approach for specific endemic settings remains challenging, particularly for countries in sSA with limited access to advanced technologies. This article examines the current strategies and tools for Plasmodium falciparum genetic diversity typing and resistance monitoring and proposes how the different tools could be employed in resource-poor settings. Advanced approaches enabling targeted deep sequencing is valued as a sensitive method for assessing drug resistance and parasite diversity but remains out of the reach of most laboratories in sSA due to the high cost of development and maintenance. It is, however, feasible to equip a limited number of laboratories as Centres of Excellence in Africa (CEA), which will receive and process samples from a network of peripheral laboratories in the continent. Cheaper, sensitive and portable real-time PCR methods can be used in peripheral laboratories to pre-screen and select samples for targeted deep sequence or genome wide analyses at these CEAs.
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Affiliation(s)
- Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Amed Ouattara
- School of Medicine, University of Maryland, College Park, Baltimore, USA
| | - Vincent P K Titanji
- Faculty of Science, Engineering and Technology, Cameroon Christian University, Bali, Cameroon
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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20
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Gomes S, Breia R, Carvalho T, Carnide V, Martins-Lopes P. Microsatellite High-Resolution Melting (SSR-HRM) to Track Olive Genotypes: From Field to Olive Oil. J Food Sci 2018; 83:2415-2423. [PMID: 30350554 DOI: 10.1111/1750-3841.14333] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022]
Abstract
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.
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Affiliation(s)
- Sónia Gomes
- School of Life Science and Environment, Dept. of Genetics and Biotechnology, Blocos Laboratoriais bdg, Univ. of Trás-os-Montes and Alto Douro, 5000-801, Vila Real, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Inst. Campo Grande, Univ. of Lisboa, C8 bdg, 1749-016, Lisboa, Portugal
| | - Richard Breia
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, 5000-801, Vila Real, Portugal
| | - Teresa Carvalho
- Natl. Inst. for Agricultural and Veterinary Research (INIAV), P.O. Box 6, 7350-951, Elvas, Portugal
| | - Valdemar Carnide
- School of Life Science and Environment, Dept. of Genetics and Biotechnology, Blocos Laboratoriais bdg, Univ. of Trás-os-Montes and Alto Douro, 5000-801, Vila Real, Portugal.,Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, 5000-801, Vila Real, Portugal
| | - Paula Martins-Lopes
- School of Life Science and Environment, Dept. of Genetics and Biotechnology, Blocos Laboratoriais bdg, Univ. of Trás-os-Montes and Alto Douro, 5000-801, Vila Real, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Inst. Campo Grande, Univ. of Lisboa, C8 bdg, 1749-016, Lisboa, Portugal
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21
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Li J, Xiong C, He X, Lu Z, Zhang X, Chen X, Sun W. Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice. Front Pharmacol 2018; 9:407. [PMID: 29740326 PMCID: PMC5928318 DOI: 10.3389/fphar.2018.00407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 04/09/2018] [Indexed: 12/15/2022] Open
Abstract
Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.
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Affiliation(s)
- Jingjian Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Chao Xiong
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xia He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zhaocen Lu
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Xin Zhang
- College of Biological Science and Engineering, Beifang University of Nationalities, Yinchuan, China
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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22
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Ahn YK, Manivannan A, Karna S, Jun TH, Yang EY, Choi S, Kim JH, Kim DS, Lee ES. Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance. Sci Rep 2018; 8:5188. [PMID: 29581444 PMCID: PMC5980001 DOI: 10.1038/s41598-018-23279-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/06/2018] [Indexed: 11/08/2022] Open
Abstract
The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.
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Affiliation(s)
- Yul-Kyun Ahn
- Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea.
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sandeep Karna
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun-Young Yang
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sena Choi
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Jin-Hee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
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Pereira L, Gomes S, Barrias S, Fernandes JR, Martins-Lopes P. Applying high-resolution melting (HRM) technology to olive oil and wine authenticity. Food Res Int 2018; 103:170-181. [DOI: 10.1016/j.foodres.2017.10.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
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Bowman S, McNevin D, Venables SJ, Roffey P, Richardson A, Gahan ME. Species identification using high resolution melting (HRM) analysis with random forest classification. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2017.1315835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sorelle Bowman
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | | | - Paul Roffey
- Forensics, Specialist Operations, Australian Federal Police, Canberra, Australia
| | - Alice Richardson
- National Centre for Epidemiology & Population Health, Australian National University, Canberra, Australia
| | - Michelle E. Gahan
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
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Jo IH, Kim YC, Kim DH, Kim KH, Hyun TK, Ryu H, Bang KH. Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars ( Panax ginseng). J Ginseng Res 2016; 41:444-449. [PMID: 29021689 PMCID: PMC5628328 DOI: 10.1016/j.jgr.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/19/2016] [Indexed: 01/09/2023] Open
Abstract
The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.
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Affiliation(s)
- Ick Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27715, Republic of Korea
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27715, Republic of Korea
| | - Dong Hwi Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27715, Republic of Korea
| | - Kee Hong Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27715, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kyong Hwan Bang
- Department of Planning and Coordination, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
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Ajamma YU, Mararo E, Omondi D, Onchuru T, Muigai AWT, Masiga D, Villinger J. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis. F1000Res 2016; 5:1949. [PMID: 27703667 PMCID: PMC5031131 DOI: 10.12688/f1000research.9224.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 01/08/2023] Open
Abstract
Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the
Anopheles gambiae and
Culex pipiens complexes. We validated the use of PCR-HRM analyses to differentiate species within
Anopheles and within each of six genera of culicine mosquitoes, comparing primers targeting cytochrome b (
cyt b), NADH dehydrogenase subunit 1 (ND1), intergenic spacer region (IGS) and cytochrome c oxidase subunit 1 (
COI) gene regions. HRM analyses of amplicons from all the six primer pairs successfully differentiated two or more mosquito species within one or more genera (
Aedes (
Ae. vittatus from
Ae. metallicus),
Culex (
Cx. tenagius from
Cx. antennatus,
Cx. neavei from
Cx. duttoni, cryptic
Cx. pipiens species),
Anopheles (
An. gambiae s.s. from
An. arabiensis) and
Mansonia (
Ma. africana from
Ma. uniformis)) based on their HRM profiles. However, PCR-HRM could not distinguish between species within
Aedeomyia (
Ad. africana and
Ad. furfurea),
Mimomyia (
Mi. hispida and
Mi. splendens) and
Coquillettidia (
Cq. aurites,
Cq. chrysosoma,
Cq. fuscopennata,
Cq. metallica,
Cq. microannulatus,
Cq. pseudoconopas and
Cq. versicolor) genera using any of the primers. The IGS and COI barcode region primers gave the best and most definitive separation of mosquito species among anopheline and culicine mosquito genera, respectively, while the other markers may serve to confirm identifications of closely related sub-species. This approach can be employed for rapid identification of mosquitoes.
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Affiliation(s)
- Yvonne Ukamaka Ajamma
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Department of Botany (Genetics), Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Enock Mararo
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - David Omondi
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Biochemistry and Molecular Biology Department, Egerton University, Egerton, Kenya; Molecular Biology and Virology Laboratory, Department of Medical Biosciences, University of Western Cape, South Africa
| | - Thomas Onchuru
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology (MPI-CE), Jena, Germany; Department for Evolutionary Ecology, Institute for Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Anne W T Muigai
- Department of Botany (Genetics), Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Daniel Masiga
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jandouwe Villinger
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
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.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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Lombal AJ, Wenner TJ, Burridge CP. Assessment of high-resolution melting (HRM) profiles as predictors of microsatellite variation: an example in Providence Petrel (Pterodroma solandri). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0327-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Juiz NA, Cayo NM, Burgos M, Salvo ME, Nasser JR, Búa J, Longhi SA, Schijman AG. Human Polymorphisms in Placentally Expressed Genes and Their Association With Susceptibility to Congenital Trypanosoma cruzi Infection. J Infect Dis 2015; 213:1299-306. [PMID: 26597259 DOI: 10.1093/infdis/jiv561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND It is currently unclear why only a proportion of children born to Trypanosoma cruzi-infected mothers acquire the infection. We have examined the association of 11 single-nucleotide polymorphisms (SNPs) located in genes coding for placental expression enzymes as genetic markers of susceptibility to congenital T. cruzi infection (hereafter, "congenital infection"): rs2014683 and rs1048988 in ALPP; rs11244787 and rs1871054 in ADAM12; rs243866, rs243865, rs17859821, rs243864, and rs2285053 in MMP2; and rs3918242 and rs2234681 in MMP9. METHODS Two groups of children born to mothers seropositive for T. cruzi were compared: 101 had congenital infection, and 116 were uninfected. Novel high-resolution melting and capillary electrophoresis genotyping techniques were designed and used. RESULTS Logistic regression analysis showed that mutations in rs11244787 and rs1871054 (in ADAM12) and rs243866, rs17859821, and rs2285053 (in MMP2) were associated with susceptibility to congenital infection. Multifactor dimensionality reduction revealed that genotyping results for rs11244787, rs1871054, rs243866, rs17859821 and rs243864 sites would be a good predictor of congenital infection. CONCLUSIONS Our results suggest an important role of human polymorphisms in proteins involved in extracellular matrix remodeling and the immune response during congenital infection. To our knowledge, this is the first study demonstrating the association between mutations in placentally expressed genes and susceptibility to congenital infection.
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Affiliation(s)
- Natalia A Juiz
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Nelly M Cayo
- Instituto de Biología de la Altura, Universidad Nacional de Jujuy
| | - Marianela Burgos
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Miriam E Salvo
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Julio R Nasser
- Laboratorio de Química Biológica, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Argentina
| | - Jacqueline Búa
- Instituto Nacional de Parasitología Dr Mario Fatala Chaben, ANLIS, Buenos Aires
| | - Silvia A Longhi
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Alejandro G Schijman
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
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High Resolution Melting (HRM) analysis in eggplant (Solanum melongena L.): A tool for microsatellite genotyping and molecular characterization of a Greek Genebank collection. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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Wu B, Zhong GY, Yue JQ, Yang RT, Li C, Li YJ, Zhong Y, Wang X, Jiang B, Zeng JW, Zhang L, Yan ST, Bei XJ, Zhou DG. Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments. PLoS One 2014; 9:e94506. [PMID: 24732455 PMCID: PMC3986212 DOI: 10.1371/journal.pone.0094506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.
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Affiliation(s)
- Bo Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guang-yan Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
| | - Jian-qiang Yue
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
| | - Run-ting Yang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chong Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yue-jia Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yun Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Bo Jiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ji-wu Zeng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Li Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shu-tang Yan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xue-jun Bei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Dong-guo Zhou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
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Druml B, Cichna-Markl M. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis. Food Chem 2014; 158:245-54. [PMID: 24731338 DOI: 10.1016/j.foodchem.2014.02.111] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 02/02/2014] [Accepted: 02/19/2014] [Indexed: 11/17/2022]
Abstract
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.
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Affiliation(s)
- Barbara Druml
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria.
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Vali Z, Raz A, Bokharaei H, Nabavi M, Bemanian MH, Yazdi MS, Djadid ND. Development of a High-resolution Melting Analysis Method Based on SYBR Green-I for rs7216389 Locus Genotyping in Asthmatic Child Patients. Avicenna J Med Biotechnol 2014; 6:72-80. [PMID: 24834309 PMCID: PMC4009098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asthma is caused by the combination of different factors. Current concepts of asthma pathogenesis emphasize on gene-environment interactions. Mega-genome scanning projects revealed that different Single Nucleotide Polymorphisms (SNPs) are related to asthma susceptibility. rs7216389-T is one of them that is related to childhood asthma and its effect on childhood asthma severity has been proved in different nations, however no study has been performed in Eastern Mediterranean and Middle East countries yet. METHODS To perform population genetic studies, a rapid and high-throughput screening method is necessary. High-resolution melting analysis is a rapid, powerful and accurate method, which is suitable for this type of studies. Therefore, it has been decided to develop a high-resolution melting method for rs7216389 locus genotyping in Iranian asthmatic children. In the current study, a high-resolution melting analysis method based on SYBR Green-I was developed to check the frequency of rs7216389-T mutation in Iranian asthmatic children for the first time. RESULTS Second and third classes of intercalating dyes are commonly used for high-resolution melting method. However, in this study, SYBR Green-I was used for rs7216389 locus genotyping for the first time. Our results for 60 samples showed that SYBR Green-I has good efficacy for rs7216389 locus genotyping through high-resolution melting method in comparison with PCR-RFLP and sequencing. CONCLUSION Comparison of our results based on HRM analysis with PCR-RFLP showed that our developed method is rapid, accurate, high-throughput and economic to study the rs7216389 locus in asthmatic children and it is applicable for other similar population genetic studies.
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Affiliation(s)
- Zahra Vali
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran,Department of Pediatrics, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Abbasali Raz, Ph.D., and Navid Dinparast Djadid, Ph.D., Malaria & Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +98 21 66480780, Fax: +98 21 66465132. E-mail:;
| | - Hanieh Bokharaei
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Nabavi
- Department Allergy and Immunology, Hazrate Rasoul Akram Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hassan Bemanian
- Department Allergy and Immunology, Hazrate Rasoul Akram Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Navid Dinparast Djadid
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Abbasali Raz, Ph.D., and Navid Dinparast Djadid, Ph.D., Malaria & Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +98 21 66480780, Fax: +98 21 66465132. E-mail:;
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