Development of SNP markers in Crassostrea hongkongensis based on the next-generation sequencing and high resolution melting analysis

2014 ◽  
Vol 6 (3) ◽  
pp. 559-562 ◽  
Author(s):  
Jiaomei Huang ◽  
Yang Zhang ◽  
Jun Li ◽  
Ziniu Yu
Keyword(s):  
Next Generation Sequencing ◽  
High Resolution ◽  
High Resolution Melting ◽  
Snp Markers ◽  
High Resolution Melting Analysis ◽  
Next Generation ◽  
Crassostrea Hongkongensis ◽  
Melting Analysis ◽  
Generation Sequencing

scholarly journals Microsatellite marker development for the tetraploid Veronica aragonensis (Plantaginaceae) using next-generation sequencing and high-resolution melting analyses

2018 ◽  
Vol 6 (5) ◽  
pp. e01154
Author(s):  
Nélida Padilla-García ◽  
Teresa Malvar-Ferreras ◽  
Josie Lambourdière ◽  
M. Montserrat Martínez-Ortega ◽  
Nathalie Machon
Keyword(s):  
Next Generation Sequencing ◽  
High Resolution ◽  
Microsatellite Marker ◽  
High Resolution Melting ◽  
Marker Development ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

2012 ◽  
Vol 50 (9) ◽  
pp. 3054-3059 ◽  
Author(s):  
M. M. Cousins ◽  
S.-S. Ou ◽  
M. J. Wawer ◽  
S. Munshaw ◽  
D. Swan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Resolution ◽  
High Resolution Melting ◽  
Next Generation ◽  
Generation Sequencing ◽  
Hiv Diversity

scholarly journals Determination ofRETSequence Variation in an MEN2 Unaffected Cohort Using Multiple-Sample Pooling and Next-Generation Sequencing

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
R. L. Margraf ◽  
J. D. Durtschi ◽  
J. E. Stephens ◽  
M. Perez ◽  
K. V. Voelkerding
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Variation ◽  
High Resolution Melting ◽  
Next Generation ◽  
Sample Pooling ◽  
Melting Analysis ◽  
Multiple Sample ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Multisample, nonindexed pooling combined with next-generation sequencing (NGS) was used to discoverRETproto-oncogene sequence variation within a cohort known to be unaffected by multiple endocrine neoplasia type 2 (MEN2). DNA samples (113 Caucasians, 23 persons of other ethnicities) were amplified forRETintron 9 to intron 16 and then divided into 5 pools of <30 samples each before library prep and NGS. Two controls were included in this study, a single sample and a pool of 50 samples that had been previously sequenced by the same NGS methods. All 59 variants previously detected in the 50-pool control were present. Of the 61 variants detected in the unaffected cohort, 20 variants were novel changes. Several variants were validated by high-resolution melting analysis and Sanger sequencing, and their allelic frequencies correlated well with those determined by NGS. The results from this unaffected cohort will be added to theRETMEN2 database.

Identification of Capsicum species using SNP markers based on high resolution melting analysis

Genome ◽  
2010 ◽  
Vol 53 (12) ◽  
pp. 1029-1040 ◽  
Author(s):  
Hee-Jin Jeong ◽  
Yeong Deuk Jo ◽  
Soung-Woo Park ◽  
Byoung-Cheorl Kang
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
High Resolution Melting ◽  
Snp Markers ◽  
High Resolution Melting Analysis ◽  
Waxy Gene ◽  
Nucleotide Polymorphisms ◽  
Cytoplasmic Dna ◽  
Melting Analysis ◽  
Capsicum Species

Single nucleotide polymorphisms (SNPs) derived from both nuclear and cytoplasmic DNA sequences were developed to identify distinct species of Capsicum . Species identification was achieved by detecting allelic variations of these type of markers via high resolution melting analysis (HRM). We used the HRM polymorphisms of COSII markers and the Waxy gene from the nuclear sequence, in addition to the intergenic spacer between trnL and trnF from cytoplasmic DNA as our SNP markers. A total of 31 accessions of Capsicum, representing six species, were analyzed using this method. As single markers were insufficient for identifying Capsicum species, combinations of all markers unambiguously identified all six. A phylogeny based on the SNP markers was consistent with the current taxonomy of Capsicum species. These observations demonstrate that the markers developed in this study are useful for rapid identification of new germplasm for management of Capsicum species.

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