Microsatellite high-resolution melting (SSR-HRM) analysis for identification of sweet cherry rootstocks in Greece

Sweet cherries can be grafted onto a wide range of rootstocks belonging to the genus Prunus. The identification of sweet cherry rootstocks using morphological traits is almost impossible particularly during the dormant season, yet it is very important for the grower to know exactly the rootstock as this has a major influence on cultivar performance and agricultural practices. However, DNA-based molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides a good opportunity to reliably distinguish the rootstocks. Herein, we have integrated high-resolution melting (HRM) analysis, coupled with five simple sequence repeat (SSR) markers, in order to facilitate the identification of the most popular sweet cherry rootstocks in Greece. The five SSR loci used were highly informative and generated a unique melting curve profile of microsatellites for each of the six sweet cherry rootstocks tested. In particular, one marker, BPPCT002, with six HRM profiles was sufficient to discriminate all the sweet cherry rootstocks studied, highlighting its potential use for rootstock identification. Hence, this assay provided a flexible, cost-effective and closed-tube microsatellite genotyping method well suited to sweet cherry rootstock identification.

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

Food Control ◽

10.1016/j.foodcont.2010.09.040 ◽

2011 ◽

Vol 22 (3-4) ◽

pp. 532-541 ◽

Cited By ~ 81

Author(s):

Ioannis Ganopoulos ◽

Anagnostis Argiriou ◽

Athanasios Tsaftaris

Keyword(s):

High Resolution ◽

Sweet Cherry ◽

High Resolution Melting ◽

Hrm Analysis ◽

Protected Designation Of Origin

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High-Resolution Melting Curve Analysis to Predict Extended Blood Group Phenotypes among Thai Donors and Patients

Transfusion Medicine and Hemotherapy ◽

10.1159/000520713 ◽

2021 ◽

pp. 1-8

Author(s):

Oytip Nathalang ◽

Kamphon Intharanut ◽

Sarisa Chidtrakoon

Keyword(s):

High Resolution ◽

Blood Group ◽

High Resolution Melting ◽

Melting Curve ◽

Melting Curve Analysis ◽

Blood Group Antigens ◽

Red Cell ◽

Nucleotide Polymorphisms ◽

Hrm Analysis ◽

Antibody Specificities

Background: High-resolution melting (HRM) analysis is an alternative method for red cell genotyping. Differences in melting curves between homozygous and heterozygous genotypes can predict phenotypes in blood group systems based on single-nucleotide polymorphisms. This study aimed to implement HRM analysis to predict additional extended blood group phenotypes in Thai donor and patient populations. Methods: Blood samples obtained from 300 unrelated Thai blood donors and 23 patients with chronic transfusions were included. HRM analysis was developed and validated in genotyping of KEL*01 and KEL*02, JK*01 and JK*02, FY*01, FY*02, and FY*02 N.01, DI*01 and DI*02, GYPB*03 and GYPB*04, RHCE*E and RHCE*e, and DO*01 and DO*02. Then genotyping results from HRM and polymerase chain reaction with sequence-specific primer (PCR-SSP) and phenotyping results were compared. Results: The validated genotyping results in known DNA controls by HRM analysis agreed with DNA sequencing. The genotyping results among 300 donors in 15 alleles by HRM analysis were in complete concordance with those obtained by serological testing and PCR-SSP. The sensitivity and specificity of the HRM assay were both 100%. Among patients, 13 had alloantibodies that possessed predicted antigen-negative phenotypes corresponding to those antibody specificities, and the highest probability of genotyped-matched donors was given to the remaining patients. Conclusions: We developed and implemented the HRM analysis assay for red cell genotyping to predict extended blood group antigens in Thai donor and patient populations. The data from this study may help inform about and support transfusion care of Thai patients to reduce the risk of alloimmunisation.

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Genotypic differentiation of Monilinia spp. populations in Serbia using a high-resolution melting (HRM) analysis

Plant Protection Science ◽

10.17221/35/2020-pps ◽

2020 ◽

Vol 57 (No. 1) ◽

pp. 38-46

Author(s):

Antonios Zambounis ◽

Eleni Stefanidou ◽

Panagiotis Madesis ◽

Jovana Hrustić ◽

Milica Mihajlović ◽

...

Keyword(s):

Genetic Diversity ◽

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Brown Rot ◽

Northern Region ◽

Monilinia Fructigena ◽

Hrm Analysis ◽

Species Specific ◽

Pathogen Populations

Monilinia laxa, Monilinia fructicola and Monilinia fructigena are the three main causal agents of brown rot, which is one of the most important diseases of stone fruits in pre- and postharvest conditions. Nowadays, the need for the precise genotyping of these Monilinia species in terms of the genetic diversity of their populations or differences in their pathogenicity and host range is a prerequisite for any efficient disease management. In our study, the genetic structure of Monilinia populations in Serbia from three geographically distinct regions was investigated employing a high-resolution melting (HRM) analysis which is a sensitive and rapid molecular approach in fungal genotyping and diagnostics. Using species-specific primer pairs genotype-specific HRM melting curve profiles were generated allowing to efficiently decipher the genetic diversity of the Monilinia populations. The Monilinia genotypes could be easily distinguished according to their melting curves. The isolates from the northern region were assigned to distinct genotypes and grouped rather independently compared to the isolates of the other two regions among all three tested Monilinia spp. M. fructicola and M. fructigena showed a higher genetic diversity among their populations (44%) compared with the genetic diversity among the M. laxa populations (7%). In contrast, the genetic variance within the pathogen populations was higher in the case of M. laxa (93%). Our data revealed an absence of host specificity in the Monilinia spp. populations.

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Identification of Four Mud Crab Species (Genus Scylla) based on High-resolution Melting (HRM) Analysis

10.21203/rs.3.rs-420600/v1 ◽

2021 ◽

Author(s):

Yongliang Li ◽

Ronghua Li ◽

Xiayue Chen ◽

Chunlin Wang ◽

Changkao Mu ◽

...

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Scylla Serrata ◽

Scylla Paramamosain ◽

Melting Curve Analysis ◽

Single Pair ◽

Crab Species ◽

Mud Crab ◽

Hrm Analysis

Abstract In this study, we described the successful identification of four mud crab species (genus Scylla) by high-resolution melting curve analysis (HRM) of single nucleotide polymorphisms (SNPs). The complete mitochondrion genome sequences of Scylla serrata, Scylla paramamosain, Scylla olivacea and Scylla tranquebarica were aligned and screened for distinct fragments. A single pair of primers were designed to amplify the 203-bp consensus amplicon. As a result, a total of 96 samples from the four mud crab species were clearly separated. The melting profiles from HRM analysis were found to be distinct across the species tested, and a number of 28 SNP sites were confirmed by sequencing. This new identification method will be a useful tool for discrimination of the four Scylla species and contribute to the effective breeding management of these species.

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High resolution melting-curve (HRM) analysis for the diagnosis of cryptosporidiosis in humans

Molecular and Cellular Probes ◽

10.1016/j.mcp.2008.10.003 ◽

2009 ◽

Vol 23 (1) ◽

pp. 10-15 ◽

Cited By ~ 49

Author(s):

Aradhana Pangasa ◽

Aaron R. Jex ◽

Bronwyn E. Campbell ◽

Nathan J. Bott ◽

Margaret Whipp ◽

...

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Hrm Analysis ◽

High Resolution Melting Curve

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Diagnostic guidelines for high-resolution melting curve (HRM) analysis: An interlaboratory validation ofBRCA1mutation scanning using the 96-well LightScanner™

Human Mutation ◽

10.1002/humu.21004 ◽

2009 ◽

Vol 30 (6) ◽

pp. 899-909 ◽

Cited By ~ 98

Author(s):

Nienke van der Stoep ◽

Chantal D.M. van Paridon ◽

Tom Janssens ◽

Petra Krenkova ◽

Alexandra Stambergova ◽

...

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Hrm Analysis ◽

High Resolution Melting Curve ◽

Interlaboratory Validation

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Identification of new avian Infectious Bronchitis virus variants in Iranian poultry flocks by High Resolution Melting curve analysis

Journal of the Hellenic Veterinary Medical Society ◽

10.12681/jhvms.16425 ◽

2018 ◽

Vol 69 (1) ◽

pp. 783 ◽

Cited By ~ 1

Author(s):

A. MASOUDIAN ◽

N. SHEIKHI ◽

M. H. BOZORGMEHRI-FARD

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Melting Curve Analysis ◽

Nucleotide Sequencing ◽

Infectious Bronchitis ◽

Hrm Analysis ◽

High Resolution Melting Curve ◽

Performance Reduction ◽

Pcr Products

Avian Infectious bronchitis (IB) is a common coronavirus infection of chickens and responsible for performance reduction and increasing mortality due to subsequent respiratory, renal and/or reproductive disorders. Classification of causative agent is necessary to plan successful vaccination strategies to prevent the infection due to poor inter-strains cross-reaction. To identify dominant circulating strains in Iran, a Real-time PCR combined with 3’ Un-Translated Region (3’ UTR) High Resolution Melting (HRM) analysis designed as a rapid and reliable method for IB Virus (IBV) detection and differentiation. Samples collected from 20-suspected flocks and after PCR products, HRM curves of samples as well as 6 commercial IB live vaccines with 2 standard strains, were analyzed as references. IBV genomes detected in 11 samples while according to HRM analysis and calculating Genotype Confidence Percentage (GCP), 6 positive specimens identified as 793/B field strains and the left 5 found as new IBV variant strains. Then obtained PCR products sent for nucleotide sequencing to determine genotype relativity. All five infectious agents, related to QX-like type and indicating circulation of new variants in Iran as a probable cause of vaccination failures and consequent economical losses.

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High-resolution melting curve (HRM) analysis to establish CYP21A2 mutations converted from the CYP21A1P in congenital adrenal hyperplasia

Clinica Chimica Acta ◽

10.1016/j.cca.2011.06.033 ◽

2011 ◽

Vol 412 (21-22) ◽

pp. 1918-1923 ◽

Cited By ~ 12

Author(s):

Yi-Ching Lin ◽

Yu-Chih Lin ◽

Ta-Chih Liu ◽

Jan-Gowth Chang ◽

Hsien-Hsiung Lee

Keyword(s):

High Resolution ◽

Congenital Adrenal Hyperplasia ◽

High Resolution Melting ◽

Melting Curve ◽

Adrenal Hyperplasia ◽

Hrm Analysis ◽

High Resolution Melting Curve

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Identification and Differentiation of Monilinia Species Causing Brown Rot of Pome and Stone Fruit using High-Resolution Melting (HRM) Analysis

Phytopathology ◽

10.1094/phyto-01-16-0016-r ◽

2016 ◽

Vol 106 (9) ◽

pp. 1055-1064 ◽

Cited By ~ 12

Author(s):

Antonios Papavasileiou ◽

Panagiotis B. Madesis ◽

George S. Karaoglanidis

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Melting Curve ◽

Brown Rot ◽

Rapid Identification ◽

Stone Fruit ◽

Universal Primers ◽

Melting Curve Analysis ◽

Fungal Isolation ◽

Hrm Analysis

Brown rot is a devastating disease of stone fruit caused by Monilinia spp. Among these species, Monilinia fructicola is a quarantine pathogen in Europe but has recently been detected in several European countries. Identification of brown rot agents relies on morphological differences or use of molecular methods requiring fungal isolation. The current study was initiated to develop and validate a high-resolution melting (HRM) method for the identification of the Monilinia spp. and for the detection of M. fructicola among other brown rot pathogens. Based on the sequence of the cytb intron from M. laxa, M. fructicola, M. fructigena, M. mumecola, M. linhartiana, and M. yunnanensis isolates originating from several countries, a pair of universal primers for species identification and a pair of primers specific to M. fructicola were designed. The specificity of the primers was verified to ensure against cross-reaction with other fungal species. The melting curve analysis using the universal primers generated six different HRM curve profiles, each one specific for each species. Τhe HRM analysis primers specific to M. fructicola amplified a 120-bp region with a distinct melt profile corresponding to the presence of M. fructicola, regardless of the presence of other species. HRM analysis can be a useful tool for rapid identification and differentiation of the six Monilinia spp. using a single primer pair. This novel assay has the potential for simultaneous identification and differentiation of the closely related Monilinia spp. as well as for the differentiation of M. fructicola from other common pathogens or saprophytes that may occur on the diseased fruit.

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