Single nucleotide polymorphism (SNP) discovery in the polyploid <i>Brassica napus</i> using Solexa transcriptome sequencing

SummaryThe growth of next generation DNA sequencing technologies has led to a rapid increase in sequence based genotyping, for applications including diversity assessment, genome structure validation and gene-trait association. With the reducing cost of sequence data generation and the increasing availability of reference genomes, there are opportunities to develop high density genotyping methods based on whole genome re-sequencing. We have established a skim-

show abstract

“…al. identified 41,593 SNPs between the B. napus cultivars Tapidor and Ningyou 7 based on 20 million Illumina RNA-Seq reads (Trick et al, 2009). …”

Section: Durstewitz Et Al Identified 604 Snps Using 100 Est-based Ammentioning

confidence: 99%

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…Actually, SNP discovery by RNA-Seq is an effective preliminary step towards the construction of a SNP array for a non-model species . Consequently, transcriptome sequencing has been successfully applied to characterize single nucleotide markers in several organisms, using various NGS platforms (Vera et al, 2008, Trick et al, 2009, Parchman et al, 2010.…”

Section: Snp Detectionmentioning

confidence: 99%

PERSPECTIVES Transcriptome sequencing: next generation approach to RNA functional analysis

Żmieńko¹,

Jackowiak²,

Figlerowicz³

2011

bta

View full text Add to dashboard Cite

The most general definition of transcriptome assumes that it is a complete set of RNA molecules (transcripts) that are formed in a given organism. In response to exogenous and endogenous stimuli, transcriptome undergoes constant qualitative and quantitative changes. Monitoring these changes can provide information on how the living organisms function and deal with the changing environmental conditions. Recently, a new approach, called RNA sequencing or RNA-Seq has been applied to transcriptome-oriented studies. It is based on the next-generation sequencing and allows transcript discovery and quantification. This new approach permits identification of novel transcripts and products of their processing or partial degradation. Since RNA-Seq does not require information about the sequence of the reference genome, it can be used for transcriptome analysis in any organism. This feature combined with the high sensitivity and broad dynamic range of RNA-Seq experiments, make them much more versatile for high-throughput studies as compared to DNA microarray technology.

show abstract

“…Trick et al (2009b) developed a robust method to discover SNPs through transcriptome analysis of the polyploid B. napus cultivars, Tapidor and Ningyou7, using the Illumina platform. In this case, Brassica unigene sequences were used as a reference and aligned with sequence reads using MAQ software to discover SNPs.…”

Section: Snp Discoverymentioning

confidence: 99%

Applications and challenges of next-generation sequencing in Brassica species

Wei

Xiao

Hayward

et al. 2013

Planta

View full text Add to dashboard Cite

show abstract

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing

Cited by 313 publications

References 27 publications

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

PERSPECTIVES Transcriptome sequencing: next generation approach to RNA functional analysis

Applications and challenges of next-generation sequencing in Brassica species

Contact Info

Product

Resources

About