Development of molecular markers tightly linked to Pvr4 gene in pepper using next-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.

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Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽

10.1139/g11-002 ◽

2011 ◽

Vol 54 (5) ◽

pp. 360-367 ◽

Cited By ~ 18

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.

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

Expert Review of Molecular Diagnostics ◽

10.1586/erm.13.4 ◽

2013 ◽

Vol 13 (2) ◽

pp. 151-165 ◽

Cited By ~ 28

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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Next generation sequencing technologies for the development of molecular markers and the analysis of genome diversity in Capsicum spp.

Acta Horticulturae ◽

10.17660/actahortic.2019.1242.123 ◽

2019 ◽

pp. 831-838

Author(s):

T. Cardi ◽

N. D’Agostino ◽

C. Cantarella ◽

V. Colonna ◽

B. Greco ◽

...

Keyword(s):

Molecular Markers ◽

Next Generation Sequencing ◽

Next Generation ◽

Genome Diversity ◽

Sequencing Technologies ◽

Capsicum Spp ◽

Generation Sequencing

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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

Theoretical and Applied Genetics ◽

10.1007/s00122-012-1997-1 ◽

2012 ◽

Vol 126 (2) ◽

pp. 511-522 ◽

Cited By ~ 33

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

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Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, Cenchrus longispinus L., based on next generation sequencing data

PeerJ ◽

10.7717/peerj.7965 ◽

2019 ◽

Vol 7 ◽

pp. e7965

Author(s):

JongYoung Hyun ◽

Hoang Dang Khoa Do ◽

Joonhyung Jung ◽

Joo-Hwan Kim

Keyword(s):

Molecular Markers ◽

Next Generation Sequencing ◽

Genomic Data ◽

Alien Plants ◽

Next Generation Sequencing Data ◽

Phylogenomic Analysis ◽

Next Generation ◽

Invasive Alien Plants ◽

Chloroplast Genomes ◽

Generation Sequencing

Background Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied. Methods We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers. Results In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.

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