The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Lehmensiek, A.; Sutherland, Mark W.; McNamara, Raymond B.

doi:10.1007/s00122-008-0813-4

Cited by 77 publications

(38 citation statements)

References 23 publications

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“…Allele-specific PCR assays were developed to enable direct selection of desirable fad2 and fad3 alleles in markerassisted trait introgression and breeding. In barley, SNP markers were identified that were linked to a covered smut resistance gene, Ruh.7H, by using high-resolution melting (HRM) technique [84]. In sugar beet, an anchored linkage map based on AFLP, SNP, and RAPD markers was developed to map QTL for Beet necrotic yellow vein virus resistance genes, Rz4 [85] and Rz5 [86].…”

Section: Examples In Othermentioning

confidence: 99%

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

2014

The Role of Bioinformatics in Agriculture

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The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the everincreasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.

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Section: Examples In Othermentioning

confidence: 99%

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

2014

The Role of Bioinformatics in Agriculture

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“…In this method, amplified DNA strands are melted apart via a gradual increase in temperature, and different melting patterns are detected based on subtle changes in fluorescence generated by double-stranded DNA-binding dyes. The rapid, inexpensive detection of a broad range of SNPs via HRM analysis makes this technique suitable for genotype discrimination (Lehmensiek et al 2008) and genetic mapping (Chagne et al 2008); various cultivars have been identified using SNPs via these technique (Mackay et al 2008). Therefore, in this study, we developed an effective method for identifying Korean-specific C. tricuspidata ecotypes using markers derived from plastid and nuclear DNA sequences and demonstrated that marker polymorphisms can be efficiently detected by ARMS-PCR and HRM analysis.…”

Section: Introductionmentioning

confidence: 99%

Molecular markers based on chloroplast and nuclear ribosomal DNA regions which distinguish Korean-specific ecotypes of the medicinal plant Cudrania tricuspidata Bureau

et al. 2017

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract Cudrania tricuspidata Bureau is a widely-used, medicinal, perennial and woody plant. Obtaining information about the genetic diversity of plant populations is highly important with regard toconservation and germplasm utilization. Although C. tricuspidata is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes from different countries.In this study, we developed single nucleotide polymorphism (SNP) markers derived from the chloroplast and nuclear genomic sequences, which serve to to identify distinct Koreanspecific ecotypes of C. tricuspidata via amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of twelve C. tricuspidata ecotypes from different regions using DNA sequences in the maturaseK (MatK) chloroplast intergenic region and nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

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“…BRCA1 and BRCA2 genes, Hondow et al 2011). This method has also been used to detect mutations (single-nucleotide polymorphisms, SNPs and small insertions/deletions, InDels) in plant genetic studies, including TILLING in Lycopersicon esculentum (Gady et al 2009), Oryzias latipes (Ishikawa et al 2010), Triticum aestivum (Botticella et al 2011), Brassica rapa (Lochlainn et al 2011) and genetic mapping in Hordeum vulgare (Lehmensiek et al 2008), Zea mays (Li et al 2010) and Oryza sativa (Li et al 2011). HRM has also been used for the identification of transgenic plants (Milner et al 2014) and the detection of DNA methylation (Wojdacz and Dobrovic 2007).…”

Section: Introductionmentioning

confidence: 99%

Mutation Detection by Analysis of DNA Heteroduplexes in TILLING Populations of Diploid Species

Szurman-Zubrzycka

Chmielewska

Gajewska

et al. 2016

Biotechnologies for Plant Mutation Breeding

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In the beginning of mutation research, mutations could only be detected indirectly through the analysis of the phenotypic alterations that they caused. The detection of mutations at the DNA level became possible with the development of sequencing methods. Nowadays, there are many different methods and strategies that have been created for mutation detection, both in natural and mutagenised populations. The strategies differ in accuracy and sensitivity, as well as in the laboratory facilities, time, costs and efforts that are required. The majority of them involve the pooling of DNA samples and the amplification of a gene (fragment) of interest followed by heteroduplex formation. One of the popular strategies for mutation identification takes advantage of the specific endonuclease (e.g. CEL I) that recognises and cuts heteroduplexes precisely at the 3 0 position of the mismatch site. The cleaved fragments are usually visualised through electrophoresis in a polyacrylamide gel using LI-COR sequencers, but agarose electrophoresis may also be used for this purpose, although with less sensitivity. A different mutation identification strategy, which is based on the high-resolution melting (HRM) technique, may be the method of choice when working with a short gene or a gene fragment whose length optimally does not exceed 400 bp.

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The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Cited by 77 publications

References 23 publications

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Molecular markers based on chloroplast and nuclear ribosomal DNA regions which distinguish Korean-specific ecotypes of the medicinal plant Cudrania tricuspidata Bureau

Mutation Detection by Analysis of DNA Heteroduplexes in TILLING Populations of Diploid Species

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