Tag Archives: SNPs

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

How Far Shall we go With Genetic Testing?

Map myGeneRecently I saw this sign on a house in the China Town of Singapore, advertising for “Genetic Testings for Health and Innate Talents”. Having a look on their homepage > I could find that they have two main objectives:

  1. Discovery of genetic variations that contribute to disease risk. (Disease Susceptibility Genetic Test or Genetic Predisposition Test)
  2. Discovery of genetic variations that contribute to intelligence, personality characteristics, superior athletic performance, vocal ability, dancing ability, and other areas where humans can excel. (Innate Talents & Traits Genetic Test)

Obviously a lab in the US is testing some SNPs on Affymetrix Arrays > for them. It is not clear what they are testing, especially in terms of “Innate talents”. They have some testimonials > that do not really say much. With or without knowing a genetic disposition it makes sense to take care on ones diet and exercise the body. If an inherited disease is known in the family, it is wise to be careful and observe the body. Many genetic markers are only linked to a disease at a low percentage of penetration, but there is no guarantee that the carrier develops the disease later. Often this is a severe psychological burdon and requires genetic and psychological consulting.

Even more suspicious is the testing for “Innate Talents”. What is really known about it and how far shall we go?