A targeted GBS technology for all breeding communities

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Updated : Tue, December 7, 2021 @ 10:11 PM

Originally published : Tue, Dec 07, 2021 @ 02:11 PM

The decisions made by molecular breeding programmes have a substantial impact on the world around us, from productivity of livestock to agricultural sustainability. Historically, array genotyping has provided useful data to inform these programmes. However, the need for a cost-efficient, flexible and scalable mid-plex genotyping platform has hindered advancement in genome-wide association studies (GWAS). SeqSNP is a refined type of targeted genotyping by sequencing (targeted GBS) technology that is scalable while offering flexibility in single nucleotide polymorphism (SNP) sequence selection. This technology fills the gap that exists in process flow and better serves all molecular breeding programmes.

Cost-efficient: One goal of many breeding programmes is to help overcome agricultural deficits. To do this, technology must be able to assess complex traits and be widely accessible to all modern breeding programmes. For any technology to be widely accessible, it must be cost-efficient. SeqSNP technology does not require the expensive initial investment cost that array genotyping technology does, which can be up to 38% depending on project scope. Additionally, SeqSNP is targeted with highly efficient enrichment capability, meaning it has intrinsically lower operational cost compared other techniques like whole genome sequencing (WGS). Another factor in cost efficiency is faster data generation. In molecular breeding programmes, the speed of data generation greatly impacts the potential for generating novel species variety. Unlike array technology that has slow turnaround times, SeqSNP is capable of faster data generation that fits into breeding cycles for agricultural use. 

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Flexible: For any technology to be truly applicable for all molecular breeding programmes, it must be flexible, not only with sample type, but also with application. Traditional array-based genotyping is limited by its fixed array design, which requires redesign of specific probe libraries if additional SNPs become of interest. Target enriched sequencing is the preferrable option because it has the capability to use entire probe libraries. In plant breeding, this allows for wide sequence coverage necessary to employ various crossing strategies, identify more accurate genomic estimated breeding values (GEBVs), and facilitate genomic selection (GS) strategies or GWAS. SeqSNP is a refined type of target-enriched sequencing because unlike other options, it relies on a probe library design that surrounds a targeted SNP sequence. This design allows for accommodation of minor allele frequency (MAF) and identification of de novo SNP identification in the SNP-surrounding region. Ultimately, SeqSNP has the capabilities to address the long-term breeding objectives by producing customised probe libraries in an unparalleled way.

Scalable: There is an ever-increasing demand for quality genotyping data, so the technology for all breeding programmes must be scalable to meet this need. For the same reasons the technology underlying array-based genotyping prevents flexibility, it also inhibits scalability. The technology behind SeqSNP lends itself to scalability, and in the agricultural field it has already been successfully integrated into some overall streamlined workflows. Unlike traditional array technology, SeqSNP sample processing can meet almost any need with the ability to sequence small runs to over 3,000 samples in a single sequencing lane due to its dual-index sample barcoding.

Molecular breeding communities are being limited by antiquated techniques that cannot meet rapidly evolving demands. Target-enriched sequencing offers advantages that array-based genotyping simply cannot match. Specifically, SeqSNP has the unique flexible, cost-effective, and scalable capabilities to meet the needs of all breeding programmes. Download the white paper to see how SeqSNP compares to array genotyping and how SeqSNP technology can be integrated into your breeding methods.

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LGC, Biosearch Technologies is the complete Genomics portfolio from LGC. Providing genomic analysis tools, instrumentation and services to the genomic scientific discovery sector worldwide, with focus on across ag bio, pharma and molecular diagnostics. Visit our home page to view our products and services.

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