Originally published : Mon, October 22, 2018 @ 6:14 PM
Updated : Thu, May 25, 2023 @ 11:32 AM
Plant and animal breeding programmes often take generations to improve quality and yield but using a genotyping protocol with targeted sequencing can bring you genetic gains faster. Could your plant or animal breeding programme use a boost?
Applying genomic selection methods to plant and animal breeding shortens cycle times and enables you to analyse more samples in less time, accelerating the genetic gain. Using a next generation sequencing (NGS) approach helps bring traits or new varieties to market faster, lowers costs and increases profitability.
Based on NGS, targeted genotyping by sequencing (targeted GBS) is starting to displace arrays for routine screening in breeding programs. Realising the full benefits of genomic selection means employing a targeted GBS genotyping protocol that can meet your needs in terms of multiplexing level, flexibility and cost-efficiency, while enabling you to carry out de novo SNP discovery, imputation and much more. Importantly, the time taken from library design to results can be reduced by months. Let’s look at a solution that can make all this possible.
Facing up to the need for mid-plex genotyping
Plant and animal breeders often express a need for genotyping that bridges the gap between low and high multiplexing, with comments like “we need a cost-effective way to screen 500-10,000 markers to be able to implement genomic selection and reduce time to market for new varieties.” Or “We are very interested in finding a solution for screening all of our broodstock with several thousand markers cost effectively.” Does this sound familiar?
As we saw in the previous article in this series, the sweet spot for genomic selection is around 1,000-25,000 assays run on approximately 1,000 samples. Being able to apply different levels of multiplexing using the same technology would add efficiency and consistency to your breeding program. Targeted GBS promises to fulfil these unmet needs with an accessible genomic library.
The advantages of using targeted GBS for genomic selection
Let’s briefly summarise the main advantages of using targeted GBS for genomic selection:
- Flexible and scalable marker strategy: Unlike arrays, with their fixed marker density and composition, targeted GBS methodology has the flexibility necessary for genomic selection. It can support the screening of up to 100,000 markers per sample, and still function efficiently for 500 to 25,000 markers. Additionally, oligonucleotide libraries for targeted GBS are in solution, which means that markers can be easily added to previously designed panels by adding new oligos to the library.
- Cost efficiency: NGS enables the multiplexing of thousands of samples for targeted GBS. Moreover, future developments in NGS can be expected to increase throughput and reduce costs of targeted GBS methods. Added to that, highly efficient enrichment methods can reduce day-to-day operation costs even further.
- Staying on target: Capture and sequencing to target the regions of interest significantly reduces the cost of sequencing and data analysis compared to whole genome sequencing.
- Maximising gains from imputation: Targeted GBS delivers high-quality data to support accurate and informative imputation that makes breeding strategies cost-effective.
- Turnaround times that fit into the breeding cycle: Targeted GBS enables a turnaround time of less than two weeks in the wet lab, plus no more than four weeks to design a new oligonucleotide library. This readily fits into a plant breeding cycle and can save years of development time.
- Discover de novo variants: Targeted GBS enables the discovery of new SNPs and structural variants in flanking sequences of targeted SNPs, which increases the power of genomic selection.
The question is how can these benefits be realised in the best possible way?
Fill the mid-plex genotyping gap
Our partners in the plant, livestock and aquaculture industries have helped us to understand the needs of real-world breeding programmes for targeted GBS applications for both mid-plex and high-plex resolution genotyping. The result is two capture-based sequencing options with Flex-Seq™ and Capture-Seq™, our NGS-based targeted GBS services that can help you to fully exploit the benefits of genomic selection. The hybrid capture approach utilised enables reduction in ascertainment bias and is effective for haplotype screening of complex polyploid species. To learn more about our targeted GBS solutions, contact us or request a quote.
About the author: Darshna 'Dusty' Vyas
Dusty is a Senior Scientist at LGC Biosearch Technologies specialising in plant genetics.
Her career began at the James Hutton Institute, formerly the Scottish Crop Research Institute, developing molecular markers for disease resistance in raspberries. From there Dusty moved on to Biogemma UK Ltd for a period of 13 years, where she worked primarily with cereal crops such as wheat, maize and barley. Through her participation in the Artemisia Project, funded by the Bill and Melinda Gates Foundation, at York University, she gained a vast understanding of the requirements by breeders for varietal development using molecular markers in MAS.
Dusty's goal is to further breeding programmes for global agricultural sustainability using high-throughput methods such as Flex-Seq and Capture-Seq targeted GBS.