Programmable microfluidic genotyping of plant DNA samples for marker-assisted selection

As demands to maintain the global food production continue to mount, multinational seed companies are turning to new DNA marker technologies to accelerate the rate of plant breeding and crop improvement. The key to widespread adoption of molecular breeding is the availability of flexible and cost-ef...

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Veröffentlicht in:Microsystems & nanoengineering 2018-03, Vol.4 (1), p.17097, Article 17097
Hauptverfasser: Zec, Helena C., Zheng, Tony, Liu, Lingshu, Hsieh, Kuangwen, Rane, Tushar D., Pederson, Todd, Wang, Tza-Huei
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Sprache:eng
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Zusammenfassung:As demands to maintain the global food production continue to mount, multinational seed companies are turning to new DNA marker technologies to accelerate the rate of plant breeding and crop improvement. The key to widespread adoption of molecular breeding is the availability of flexible and cost-effective tools that can perform combinatorial and high-throughput genotyping of single-nucleotide polymorphisms (SNPs) to guide the crop development process. Toward this end, we have developed a programmable, droplet-based microfluidic device for genotyping maize genomic DNA. A unique feature of the microfluidic platform is the nano sample processors (NSPs), which allow the device to sequentially load an unrestricted number of unique DNA samples using only two inlets, overcoming the current limitation to the number of sample inputs due to small device footprint. Direct and programmable droplet generation within the device allows each sample to be genotyped against a panel of markers on demand. Moreover, we have successfully implemented the Invader assay for SNP genotyping in flowing, 50-nL droplets, thus achieving significant reduction in consumption of reagents per reaction as compared with conventional genotyping platforms. As a demonstration, we performed 240 Invader reactions (testing 8 DNA samples against 10 SNP markers) and achieved greater than 93% accuracy in SNP calling of plant DNA samples in a single droplet-based experiment. Genotyping: High-throughput drops for customized crops Efforts to fast-track plant breeding may benefit from a microfluidic device that tests DNA samples with assembly line-like efficiency. Recently, the agricultural industry has turned to the large-scale analysis of plant DNA to spot markers called single nucleotide polymorphisms (SNPs) that can indicate valuable physical traits, and therefore help to propagate them without genetic modification. Tza-Huei Wang at Johns Hopkins University in the United States and colleagues report a high-speed genotyping method based on nanoliter-scale DNA droplets. The team's processing unit loads, rinses and continuously moves sample droplets through microfluidic tubes into analytical stages for on-demand screening. Because droplets flow sequentially through the device, massive data sets can be spatially tracked while retaining a small on-chip footprint. Studies of maize DNA with SNP-active probes demonstrated this approach could identify crucial gene sequences with 93% accuracy.
ISSN:2055-7434
2096-1030
2055-7434
DOI:10.1038/micronano.2017.97