CGAHR Update: Wheat Breeding Taps Next Generation Sequencing
Date Posted: January 3, 2013
This article is reprinted from the CGAHR Update, Fall 2012
With year-end funding support from the USDA-ARS Northern Plains Area Office in Ft. Collins, CO, Dr. Guihua Bai’s USDA-ARS Genotyping Lab in Manhattan, KS recently purchased a next generation bench top sequencer for discovery and implementation of high throughput markers in wheat breeding and genomics research.
Next-gen sequencers have enormous capacity and were designed to be able to sequence the entire human genome in about a day for $1,000.
There are several different Next-gen sequencing systems available, but this particular system uses a special chip for high-throughput sequencing.
The chip is based on semiconductor technology similar to that found in digital cameras, but instead of capturing light, the chip "sees" chemistry as it happens in real time. Digital data are translated directly into DNA sequence data.
In a 4 hour run, the sequencer can provide up to 80 million sequence reads at up to 200 bases per read.
The wheat genome is about five times the size of the human genome and has the largest genome size among crop species.
Unlike most other important crop species, the complete assembled wheat genome sequence is not yet available, thus limited DNA markers are currently available for wheat breeding.
Next-gen sequencing technology provides a new opportunity for marker discovery.
Using a new technique called genotyping by sequencing we can simultaneously discover tens of thousands of markers and analyze them in a breeding population in one step.
Dr. Bai’s lab will use the sequencer to perform genotyping-by-sequencing for mapping wheat genes and for genotyping breeding lines for wheat breeding programs.
The data production rate will be many orders of magnitude faster than the previous generation technologies.
With all this new speed, it seems like wheat breeding is engaging the warp drive engines!
For more information, contact Dr. Robert Bowden,(785) 532-2368, Robert.Bowden@ars.usda.gov