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.