High‐resolution melt analysis to identify and map sequence‐tagged site anchor points onto linkage maps: a white lupin (<i>Lupinus albus</i>) map as an exemplar

Croxford, Adam E.; Rogers, Tom D.; Caligari, P. D. S.; Wilkinson, M. J.

doi:10.1111/j.1469-8137.2008.02588.x

Cited by 70 publications

(45 citation statements)

References 113 publications

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“…Because of these benefits, HRM has already been used in many investigations including the detection of SNP mutations (Margraf et al 2006;Wu et al 2008), RNA editing (Chateigner-Boutin and Small 2007), identification of transgenic plants (Akiyama et al 2009), varietal identification (Mackay et al 2008), and food traceability (Ganopoulos et al 2010;Jaakola et al 2010). HRM analysis has also been successfully used for genetic mapping in white lupin, barley, apple, and almond (Chagné et al 2008;Croxford et al 2008;Lehmensiek et al 2008;Wu et al 2009). It has also been used to develop a genetic map of SNP markers in Cryptomeria japonica (Ujino-Ihara et al 2010).…”

Section: Introductionmentioning

confidence: 97%

“…HRM has been proved suitable for detecting not only SNP markers but also STS and SSR markers (Croxford et al 2008;Mackay et al 2008). In this study, HRM analysis is employed to develop markers with currently widely used SSRs and STSs, to help make full use of those existing resources to improve the efficiency of rice gene mapping and associated tasks.…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of High-Resolution Melting for Gene Mapping in Rice

Wang

Dong

et al. 2011

Plant Mol Biol Rep

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In this study, high-resolution melting (HRM) analysis was evaluated for gene mapping in rice with sequence-tagged site (STS) and simple sequence repeat (SSR) markers. A total of 103 out of 353 normal STS and SSR markers revealed polymorphic melting curves among the parental genotypes, and 12 of these were successfully used to genotype the F 2 mapping population for HRM analysis. Additional electrophoresis findings demonstrated that HRM genotyping matched with traditional electrophoresis results. To optimize the HRM-marker screening efficiency, different HRM reaction conditions were evaluated. A 5-μl touchdown-polymerase chain reaction (PCR) system provided no significant improvement in screening efficiency but in a 10-μl touchdown-PCR system, the marker screening efficiency increased by 75%. Twenty-one markers were obtained for mapping purposes under the optimized reaction conditions. This study indicates that HRM analysis can speed up the gene mapping progress in rice, while saving a lot of manpower.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Evaluation of High-Resolution Melting for Gene Mapping in Rice

Wang

Dong

et al. 2011

Plant Mol Biol Rep

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“…HRM has been proved to be an accurate, time-saving and cost-eVective approach for SNP detection in comparison to traditional gel-based methods such as RFLP and SSCP (Liew et al 2004;Wu et al 2008). HRM has been used recently to map SNP markers in plant species and gene scanning for disease-related mutations in humans (Chagne et al 2008;Croxford et al 2008;Lehmensiek et al 2008;Kennerson et al 2009). In our study, 12 putative almond genes anchored by SNP were mapped using the HRM technique, and we found this methodology to be accurate and eYcient during the laboratory, scoring and data processing phases of the work.…”

Section: Discussionmentioning

confidence: 98%

“…Recently, this approach has been applied to genetic mapping (Chagne et al 2008;Croxford et al 2008;Lehmensiek et al 2008;Kennerson et al 2009). It has been used for mutation scanning of large multi-exon genes to identify disease-related mutations in humans (Kennerson et al 2009) or linkage map construction in plant species (Chagne et al 2008;Croxford et al 2008;Lehmensiek et al 2008).…”

Section: Introductionmentioning

confidence: 98%

Mapping SNP-anchored genes using high-resolution melting analysis in almond

Tavassolian

Rabiei

et al. 2009

Mol Genet Genomics

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Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies.

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“…HRM allows melt profiles of 96 or 384 different PCR products to be achieved in minutes, compared to at least 12 h for most gelbased methods (Tindall et al, 2009). HRM analysis has primarily been used for the discovery and genotyping of single nucleotide polymorphisms (SNPs) (Graham et al, 2005), but it has also been used for precise amplicon verification (Erali et al, 2006), sequence matching applications such as HLA identity (Zhou et al, 2004) and generating STS markers in linkage mapping studies (Croxford et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

High resolution melting as an alternative method to genotype diacylglycerol O-acyltransferase 1 (DGAT1) K232A polymorphism in cattle

Abdolmohammadi¹,

Atashi²,

Zamani³

et al. 2011

CZECH J ANIM SCI

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PCR-RFLP analysis is a common method for genotyping the DGAT1 K232A polymorphism in cattle. Our purpose was to develop a high resolution melting (HRM) assay in order to genotype the polymorphic alleles. Firstly, the PCR-RFLP method was used and the 411 bp products including the DGAT1 polymorphism were digested by CfrI enzyme. Direct sequencing was performed to confirm genotypes of the K232A polymorphism for 30 samples that presented different PCR-RFLP patterns. It was determined according to sequencing results that partial enzyme digestion had occurred for some samples. A 130 bp fragment including the polymorphism was amplified for real time PCR. Then, the HRM analysis was carried out using two fluorescent dyes, SYBR Green I and EvaGreen TM . Although the HRM genotyping using SYBR Green I was contradicted by the sequencing results, three correct melting curves were obtained for the K232A polymorphism when EvaGreen TM was used. There were no false genotypes and all genotypes were in agreement with their sequencing results. The difference in the T m between the two homozygous groups was about 0.5°C and the AA genotypes showed a higher T m than the KK genotypes. The heterozygous genotypes showed a different pattern. Similar results were obtained from different concentrations of EvaGreen TM in the reactions. All 206 DNA samples were genotyped using this fluorescent dye with estimated allele frequencies of 0.66 and 0.34 for the A and K alleles, respectively. Our study showed that HRM analysis will be applicable for genotyping the DGAT1 K232A polymorphism in large populations of dairy cattle.

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High‐resolution melt analysis to identify and map sequence‐tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar

Cited by 70 publications

References 113 publications

Evaluation of High-Resolution Melting for Gene Mapping in Rice

Evaluation of High-Resolution Melting for Gene Mapping in Rice

Mapping SNP-anchored genes using high-resolution melting analysis in almond

High resolution melting as an alternative method to genotype diacylglycerol O-acyltransferase 1 (DGAT1) K232A polymorphism in cattle

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