Application of a new generation of Fluidigm microfluidic chip PCR technology in agriculture

Fish – what I want

Jim Seeb, research director at the Alaska Fisheries Agency, and his wife, Lisa, used SNPs as genetic markers to identify salmon populations about 20 years ago to manage the fishing industry. In the first year of 2008, Alaska Genetics Laboratory used Applied Biosystem's 384-well PCR system to genotype approximately 30,000 salmon. For example, 45 SNPs can be identified, but 1,350,000 data points (45x30,000) are also generated. For example, using traditional 384-well plates and single-channel PCR, 45 384-well plates can only process 384 samples, all samples need A total of 3516 plates and a large number of reagents in 78x45 blocks! But when they discovered Fluidigm's BioMark system, they could detect 96 SNPs at a time, greatly improving the quality of the experiment, using a very small amount of reagents and a BioMark Dynamic Array to simultaneously analyze 96 SNPs in 96 different samples. Point (9216 data). “This is a simpler and less error-prone workflow,” says Seeb. The lab now conducts 16 chips per day on nine Fluidigm PCR machines, four days a week, and plans to genotype 200,000 salmon in 2011. “Without this technology, we are simply unable to accomplish such a task,” said Bill Templin, chief genetics expert at the Fisheries Department.

Cattle - I want it, fish and cattle are also available!

In the spring of 2009, Curt Van Tassell, a genetics expert at the US Department of Agriculture, was looking for a way to genotype every cow in the world. In the past 10 years, Curt has studied the SNPs of hundreds of important dairy cows, hoping to find out the relationship between growth rate, milk production, cow health and longevity. Curt worked with Illumina in the US to develop a 3μm microsphere chip with 54,000 SNPs in 2007 and quickly applied the technology to the screening of dairy bulls. However, with this technology, the cost of identification for each bull is about $150-200, which is so expensive, but many bulls also receive molecular breeding tests to help farmers estimate the value of the bull. In order to extend the technology to every cow, every small-scale farm, or even a third world country such as Africa, the cost needs to be greatly reduced. So, in the spring of 2009, when Curt knew about Fluidigm's genotyping platform from a salmon company and seed genotyping company, he immediately contacted Fluidigm. However, Curt requires a cheap enough tool for the world's poorest farms like Africa, and the cost needs to be lower than Fluidigm's existing platform! In order to reduce costs to “1/3 to 1/5 of the cost of each data now”, Fluidigm finally launched the world's first reusable microfluid in early July 2010 after nearly a year of hard work. chip. Using reusable chips, the cost per data point is approximately $0.02. The desire to have a data point of 1 pence from Fluidigm may be achieved when the second generation of reusable chips is born.

Seed – the basis for the success of farmers!

Enza Zaden, the world's leading supplier of quality vegetable seeds for agriculture, chose Fluidigm's BioMarkTM system and the new 96.96 Dynamic Array to ensure the quality of its seed supply. In terms of global food supply, the demand for high-yield and disease-resistant crops is growing. Therefore, the market still urgently needs all kinds of high-quality seeds to grow delicious and nutritious vegetables. Different soil properties and climatic zones can affect crop growth, and our planet is no longer the same type of seed that meets everyone's needs. Faced with this situation, Enza Zaden uses genetic-based marker-assisted screening techniques to select and test hundreds of thousands of seeds to ensure that crop products that meet people's tastes are grown and the right varieties are available. Breeding to meet everyone's needs.

Humans and diseases?

Since the Human Genome Project was released in 2001, scientists have attempted to correlate SNPs with human characteristics and disease through GWAS research. Despite the large amount of money and time spent, many GWAS studies do not reveal very well the close relationship between them. Therefore, scientists urgently need a tool to verify the association of a disease with SNPs. What is needed is a tool that can be quickly verified and reproducible. “If you are doing large-scale validation experiments, you need the cheapest, high-quality results,” is the chief genomics expert at the Wellcome Trust Centre for Human Genetics at the University of Oxford. Jiannis Ragoussis said. Some research institutes have begun to use Fluidigm's chips for the study, including the National Cancer Institute (NCI), which is conducting a follow-up study of prostate cancer GWAS at 60 SNP sites and 15,000 samples. "The chip may be able to play its role in a broader field," Ragoussis added. If researchers prove that nearly 100 SNPs, such as 50-100, can provide useful information for doctors, then one day, there will be cancer chips, diabetes chips, heart disease chips...

Adapted: http://classic.the-scientist.com/article/display/57843/