Targeted GBS solutions workflows accelerate genomic cattle-breeding programs

Genomic technologies like genotyping by sequencing and next-generation sequencing bring value to genomic breeding programs

3 January 2023

4 minute read

By: Thermo Fisher Scientific

Advancements in genomic technologies are accelerating breeding programs by enabling higher-throughput genotyping across large populations. For example, targeted GBS (genotyping by sequencing) solutions help breeders leverage the power and insights available from next-generation sequencing (NGS) in a cost effective way. NGS delivers plant and animal genotypes at a low cost per sample with high throughput. Accessing data from these tools produce data quickly—typically within three days—so breeding programs of all types benefit from rapid decision-making.

Angela Burrell, a scientist in Thermo Fisher Scientific’s agrigenomics research and development division, is one of the people behind AgriSeq GBS solutions. In a recent interview, she explained how advances in this exciting molecular technology increase value for genomic breeding programs.

Angela’s recent work on GBS tools and workflows has so far resulted in commercialization of two ready-to-use AgriSeq products: an agriculture-specific library-prep workflow that enables high throughput, genotyping with manual or automated liquid handling, and a bovine parentage panel that verifies offspring pedigrees.

Library prep pools hundreds of samples

The AgriSeq Library Kit is designed for high-throughput amplicon preparation before targeted GBS. As Dr. Burrell explains, using this approach gets the sample DNA into the right size for sequencing. More importantly, the preparation also labels the sample DNA with specific barcodes that tag the samples. This means that each sample is tagged and can therefore be tracked through the multiplexed GBS analysis.

Angela and her team have validated the library kits, showing that they give highly uniform and reproducible results across all samples. Since the kit works with both 96- and 384-well plate formats and combines well with automation, a customer can pool hundreds of samples for sequencing in just three hours of prep.

Bovine marker analysis confirms parentage

Angela’s work with validating sequencing panels for customers and commercialization led to development of a targeted GBS panel for bovine parentage. The kit covers 200 SNPs (single nucleotide polymorphisms) recommended as molecular markers by the ISAG (International Society of Animal Genetics). These cover identification of many genomic features across a wide number of commercial cattle breeds worldwide.

Validation studies conducted by Angela and her team show that mean call rates for the parentage plate exceed 98%, with mean read uniformity at around 97.8%. They repeated the testing using samples from 96 individuals. The team also tested across different breeds, finding no difference in call rates between breeds. Reproducibility testing confirmed intra- and inter-assay consistency, with CVs greater than 99.9% for both. Furthermore, the data showed greater than 99% concordance with other methods of DNA analysis.

In combination, library prep for targeted GBS with the HTSC Kit and parentage panel deliver fast and accurate results, especially when teamed with an automated system such as the Ion GeneStudio™ S5 System for NGS. Workflow studies show a hands-on time of 15 minutes for template preparation, and then 15 minutes each for sequencing and data analysis. With the flexibility built in, targeted GBS allows researchers to pool hundreds of samples in a single sequencing run that can target hundreds or thousands of markers. This means that it is possible to run four 384-well plates per day, obtaining sequencing results in three days.

Fast results accelerate breeding decisions

As Angela explains, using the older 540 Ion Chip, throughput could be up to 1,536 samples per day, which translated into 2.3 million genotypes analyzed. She also notes that through workflow research, the team has reduced sample and reagent volume requirements, leading to greater savings and efficiency. Today, the number of possible samples and genotypes has increased even more with the introduction of the Ion 550 Chip, with the number of genotypes reaching up to 2.6 million.

As a streamlined and cost-effective tool, targeted GBS for bovine genotyping and parentage determination is a valuable addition to genomic breeding programs. The AgriSeq kits give consistent genotyping results with fast turnaround and at low cost per sample. Breeders get results quickly for parentage identification, and with targeted GBS’s ability to target additional markers, custom panels can be created to enable identification of additional markers of defective or beneficial traits.

If you would like to find out how targeted GBS can help your agricultural breeding program, please sign up for free consultation with one of our genomics professionals.