Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding

2012 ◽  
Vol 126 (2) ◽  
pp. 511-522 ◽  
Author(s):  
Huaan Yang ◽  
Ye Tao ◽  
Zequn Zheng ◽  
Di Shao ◽  
Zhenzhong Li ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Disease Resistance ◽  
Next Generation Sequencing ◽  
Marker Assisted Selection ◽  
Rapid Development ◽  
Lupinus Angustifolius ◽  
Next Generation ◽  
Stem Blight ◽  
Blight Disease ◽  
Generation Sequencing

The applications of next-generation sequencing (NGS) in drug development for cancer therapy

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Cancer Therapy ◽  
Target Identification ◽  
Rapid Development ◽  
Next Generation ◽  
Biomedical Sciences ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

2014 ◽  
Vol 12 (S1) ◽  
pp. S83-S86 ◽  
Author(s):  
Yul-Kyun Ahn ◽  
Swati Tripathi ◽  
Young-Il Cho ◽  
Jeong-Ho Kim ◽  
Hye-Eun Lee ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Sequence Variant ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Chilli Pepper ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 360-367 ◽  
Author(s):  
Tae-Hwan Jun ◽  
Andrew P. Michel ◽  
M.A. Rouf Mian
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Ssr Markers ◽  
The United States ◽  
Soybean Aphid ◽  
Genomic Sequences ◽  
Next Generation ◽  
Soybean Aphids ◽  
Genomic Ssr ◽  
Generation Sequencing

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.

scholarly journals Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Abinaya Manivannan ◽  
Jin-Hee Kim ◽  
Eun-Young Yang ◽  
Yul-Kyun Ahn ◽  
Eun-Su Lee ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Disease Resistance ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
The Impact ◽  
Generation Sequencing

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

scholarly journals Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

2015 ◽  
Vol 35 (4) ◽  
Author(s):  
Zübeyir Devran ◽  
Erdem Kahveci ◽  
Ercan Özkaynak ◽  
David J. Studholme ◽  
Mahmut Tör
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-generation sequencing: a powerful tool for the discovery of molecular markers in breast ductal carcinomain situ

2013 ◽  
Vol 13 (2) ◽  
pp. 151-165 ◽  
Author(s):  
Hitchintan Kaur ◽  
Shihong Mao ◽  
Seema Shah ◽  
David H Gorski ◽  
Stephen A Krawetz ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Ductal Carcinomain Situ ◽  
Carcinomain Situ ◽  
Generation Sequencing
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