Tag Archives: Floragenex

Interview With Dr. Georg Gradl About Genome Sequencing

georg_gradl_lowBehind the scene…

You may know that Floragenex and Eurofins MWG Operon launched a new partnership to promote RAD sequencing.

As part of Floragenex’ series of interviews on genomic applications, they talked to our colleague and NGS expert Dr. Georg Gradl about his experiences with de novo genomic sequencing.

Check out the interview

De Novo Genome Sequencing of Sunflower Via RAD-Seq

sunflowerDear NGS Expert Blog reader,

As part of our ongoing series of posts on RAD sequencing, I wanted to share some results from a recently published study describing the use of RAD-Seq for high throughput SNP development in Helianthus annuus (Sunflower).

Sunflower is one of the leading oilseed and confectionery crops in North America, with an annual crop mass of approximately 1 billion kilograms and an economic value over 720 million USD. Despite the economic importance of sunflower, relatively modest genomic resources exist for molecular genetic and marker assisted breeding applications.

To accelerate genomics resource development in sunflower, Floragenex was tasked with rapidly identifying a large set of single nucleotide polymorphism (SNP) markers in North American sunflower through the use of RAD sequencing. The end goal was to translating those markers into a downstream genotyping assay, which could be used for high-throughput applications such as linkage and association mapping.
Some highlights on this study:

  • RAD-Seq was used to rapidly construct over 15.1 Mb of de novo sunflower genomic sequence, comparable in size to a small eukaryotic transcriptome.
  • There were over 94,000 putative SNP markers identified from analysis of six sunflower lines sequenced via RAD-Seq.
  • 16,467 of these variants were incorporated into an Illumina Infinium Genotyping Array.

The above study elegantly demonstrates how RAD is an incredibly efficient marker discovery tool. From just under half a lane of Illumina data (44M 2x80bp reads), a marker resource of over 16 thousand high quality variants could be rapidly generated and deployed for breeding applications.

The full article, entitled “De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach” can be found on BMC Genomics.

As a co-author on the publication, I would be happy to answer any of your questions on this paper, so don’t hesitate to post them. For my next NGS blog entry, I’ll be showing you some interesting publication trends seen with RAD sequencing.

Cheers,
Rick Nipper
President, Floragenex

RAD-Seq Expert Blogger: Welcome Rick Nipper

Dear reader,

As a new author here at the NGS Expert Blog, I wanted to take a few minutes to introduce myself, company and the cutting-edge genomics technology my team specializes in.

My name is Rick Nipper and I am the President of a company called Floragenex. You can learn a bit more about my scientific background on LinkedIn.

rad-seqOver the past 5 years, I’ve worked with the dedicated group at Floragenex to provide genomic services around a new and innovative technology called RAD Sequencing (RAD-Seq).

What is RAD-Seq? RAD stands for Restriction site Associated DNA Sequencing. At it’s core, RAD-Seq is a genomic sequencing strategy. The concept combines a unique library prep protocol with Illumina NGS, to sequence anywhere from 0.1 to 10% of a selected genome. This “complexity reduction” approach to sequencing a genome offers significant advantages compared to other common NGS approaches:

  1. Dynamic. RAD-Seq provides the ability to examine thousands to tens of thousands of genetic loci simultaneously across a genome, depending on your research need.
  2.  Flexible: RAD-Seq has been used as an effective tool across a variety of molecular studies across genetic marker identification, population genetics, linkage mapping, phylogenetics and genome selection
  3.  Speed: RAD-Seq can offer significant time-savings compared to alternative methods.
  4.  Bioinformatics: RAD-Seq projects usually require less next-gen sequencing than other approaches, leading to faster and more streamlined analysis.
  5.  Cost:  Because RAD-Seq is designed to examine a smaller fraction of a genome, it is an economical and cost-effective method for next-gen sequencing of hundreds of samples.

Want to know a bit more about RAD-Seq and how it is being used? There are over 70 publications showcasing the use of the technology. Here are a few I’ve personally been involved in over the years:

Drop me a line if you have any questions about these publications. In the next few months, I’ll continue to post here, highlighting interesting uses of RAD-Seq in the literature, how the technology can help drive research and talking more about some publications in which we’ve been involved.

Cheers,
Rick Nipper
President, Floragenex