You’re probably aware that advances in genomic technology already reduce time and cost in molecular breeding programs. High-throughput analysis in larger populations accelerates genotyping results into real-world applications, and bar coding samples is one of the approaches currently in use.
However, if you’re struggling to understand how bar coding can help maximize efficiencies in your molecular breeding programs for agriculture, Thermo Fisher R&D scientist Michelle Swimley can help.
“Think of these bar codes as unique tags or identifiers that get attached to amplicons or DNA you are about to sequence,” she explains. “For pooled samples, this means that the individual reads associated with each sample can then be differentiated.”
Swimley, who works in genotyping by sequencing, or GBS, within Thermo Fisher Scientific’s agrigenomics group, has helped develop an additional set of 384 bar codes for the Applied Biosystems AgriSeq workflow. Combining these identifiers with the existing set means that now customers can save time and costs by sequencing up to 768 samples pooled into a targeted GBS run.
The bar codes Swimley describes are unique pieces of DNA that facilitate sample pooling in targeted GBS runs; instead of examining samples individually for molecular markers, users can now pool hundreds in the AgriSeq workflow. Using the bar code kits doubles capability, and since labeling takes place before library cleanup, it further maximizes efficiency by saving reagents and reducing hands-on pipetting time. The net effect is a cost saving per sample.
For breeding programs, this efficiency is important; scientists can now effectively process up to 1,536 samples with around 1,500 markers per day using the AgriSeq targeted GBS system within an automated next-generation sequencing (NGS) platform.
To evaluate, validate and determine the compatibility of the new bar codes with the existing set, Swimley and her team tested performance across a wide variety of different molecular panels, including corn, cucumbers and soybean. Looking at various performance indicators, they found not only that the data showed high call rates, but that results were consistent across both sets of bar codes. There was no statistical difference in mean call rates between the old and new bar code kits.
Other performance indicators showed that in terms of visibility and consistency, AgriSeq GBS covered all bar codes equally. The validation studies found no difference in the mean proportions of mapped reads, showing that ligation efficiency was consistent across all bar codes. Using both bar code kits together did not bias results. Overall, these performance metrics are important factors when considering use of bar coded samples and GBS for high-throughput GBS.
Overall, GBS and NGS technique innovation, as found in products from the Thermo Fisher Scientific agrigenomic range, helps crop science. Large-scale, high-throughput, low-cost approaches like the AgriSeq targeted GBS technology facilitate rapid breeding programs for faster phenotypic selection. Products such as the Applied Biosystems AgriSeq HTS Library Kit used in conjunction with bar code kits help maximize data output without increasing hands-on time.
To find out how our solutions can enhance your crop breeding programs, schedule a free consultation with a genotyping specialist.
For research use only. Not for use in diagnostic procedures.