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Revolutionising Peanut Cultivar Development with SNP Genotyping

Unlocking the full potential of peanuts with SNP genotyping and allele-specific PCR

3CR was delighted to host the Industry Workshop ‘Accelerating Crop and Animal Breeding Enhancement Through High-Throughput Genotyping’ at the 31st Plant and Animal Genome Conference in San Diego, USA in January this year. Professor Jeff Dunne and Dr Ryan J Andres from the Peanut Breeding & Genetics Program, Crop & Soil Sciences at, North Carolina State University, took us through their efficient and economical marker-assisted selection pipeline for peanut cultivar development which can be applied to any trait in any organism in ‘Advancing Peanut Cultivar Development: Integrating PACE reagents and User-Friendly Computational Tools for Marker-Assisted Selection’. Here is their story.

In the heartland of North Carolina, a team of scientists at NC State University is spearheading a revolution in peanut breeding. Their mission? To unlock the full potential of Virginia-type peanuts through the power of the modern genomics tools Whole Genome Sequencing and Genomic Selection using SNP Genotyping with PACE Allele-specific PCR.

Why Virginia-Type Peanuts Matter

Virginia-type peanuts, (Arachis hypogaea subsp. Hypogaea) constitute a significant portion of the U.S peanut market, prized for their in-shell products and nutritional value. With their large, visually appealing pods and seeds, they’re the darlings of gourmet snack products. However, to ensure their continued success, its crucial to enhance their resilience and productivity.

Enter Marker-Assisted Selection

Marker-Assisted Selection (MAS) is now a not-so-secret weapon in the arsenal of modern breeders. By identifying and selecting for desirable traits at the molecular levels, MAS accelerates the breeding process, producing superior cultivars with unmatched efficiency. The team have packaged their greenhouse-based, marker-assisted selection pipeline into a user-friendly toolset including open-source, python-based robotics for lab work, custom web-based applications, and PACE genotyping reagents. It is flexible, low-cost, and quick.

Harnessing SNP Genotyping by Allele-Specific PCR for Marker Development

Central to their approach, is the integration of SNP genotyping by allele-specific PCR, a rapid, cost-effective way to develop and validated trait marker assays, initially to identify and track wild species introgression blocks in germplasm and cultivars and then for widespread application of marker-assisted selection. With the PACE reagents and user-friendly computation tools designed by Prof Jeff Dunne and Ryan Andres and their colleagues, the group can swiftly analyse genetic data, pinpointing the traits that matter most for their cultivar development. Armed with a validated set of PACE markers, MAS becomes a potent tool for selecting introgression blocks conferring pathogen resistance and other valuable traits. The team designs and uses 100s of PACE assays per year.

SNP Genotyping Pipeline

The process begins with the design and ordering of primers for PACE genotyping assays. These primers are then mixed into marker assays using automated systems, streamlining laboratory workflow. Next comes DNA extraction and normalisation, followed by the crucial step of running PCR plates. Finally, data analysis using custom web applications completes the cycle, enabling the team to make informed selections based on genetic markers.

Open-Source Web Applications for analysing SNP genotyping data

Accessibility is key, and the team has developed open-source web applications including a web-based SNP caller for analysing SNP genotyping data. The application is free for anyone to use, and it can be accessed at go.ncsu.edu/snp-caller

Analysing Peanut Populations with Mixed Wild and Cultivated Genetics at University of Georgia

The NCSU peanut breeding team is not the only group applying achieving success by integrating PACE genotyping into their workflow. A group from Institute of Plant Breeding, University of Georgia have just published a paper using PACE to analyse the movement of traits between wild and cultivated peanut lines. They demonstrated that when incorporating beneficial traits from wild germplasm, unadapted wild pod and seed traits are also inherited. A major pod construction QTL was discovered in a backcross population harbouring wild-derived segments. PACE markers were developed and validated for MAS against wild-type deep pod construction traits in future cultivars.

The Future of Breeding

With MAS powered by SNP genotyping and PACE Allele-Specific PCR, the future of peanut breeding has never looked brighter. By combining traditional breeding practices with state-of -the-art genomic tools, NC State University and University of Georgia are paving the way for a new era of peanut cultivar development. And as they continue to refine and share their knowledge, the benefits can extend far beyond peanut breeding– reshaping breeding and trait development for generations to come.

Empowering Breed Improvement Programs

The culmination of these efforts serves as a blueprint for breeding programs worldwide. By demonstrating the efficacy of their pipelines and user-friendly tools for peanut breeding programs, the teams show how accessible and efficient genomics-assisted breeding can be for any trait and any organisms. With a robust framework in place, the possibilities are limitless. From swift responses to evolving biotic and abiotic threats, to the development of superior cultivars for public consumption, genomics assisted breeding holds the key to unlocking the full potential of this valuable crop and beyond.

References

Newman, C.S., Andres, R.J., Youngblood, R.C., Campbell, J.D., Simpson, S.A., Cannon, S.B., Scheffler, B.E., Oakley, A.T., Hulse-Kemp, A.M. and Dunne, J.C., 2023. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science, 13, p.1073542.

Andres, R.J. and Dunne, J.C., 2022. Understanding variation in oleic acid content of high-oleic Virginia-type peanut. Theoretical and Applied Genetics, 135(10), pp.3433-3442.

Ballén‐Taborda, C., Maharjan, N., Hopkins, M., Guimarães, L.A., Lindsey, D., Bertioli, D.J. and Leal‐Bertioli, S.C., 2024. A study of pod constriction in a peanut population with mixed wild and cultivated genetics. Crop Science.

SNP Genotyping to revolutionise peanut cultivar development
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MEET OUR TEAM

Steve Asquith Managing Director
Steve began his career in the Genetics Division of GlaxoSmithKline, as part of the team establishing GSK’s high-throughput core genotyping laboratory. Steve joined KBioscience when it was first founded in 2002 and was a key driver in taking the company from a small start-up to a multi-national service laboratory, quickly growing the company’s revenue to over $7.5M p.a. Following the acquisition of Kbioscience by LGC in 2011, Steve was appointed Global Director of Operations for LGC Genomics, responsible for over 100 staff in Europe and N. America, successfully elevating the genotyping products and service business. Steve held a crucial leadership role until he left in 2016. In 2017 Steve joined forces with John Holme to create 3CR Bioscience, a new company with a mission to deliver outstanding, customer-focused genotyping products with innovation and affordability at its core.
Dr. John Holme Technical Director
John joined KBioscience shortly after it was founded, in 2003, and became Head of Technical Development, building the company’s genotyping and DNA extraction product portfolio and service delivery until 2011 when it was acquired by LGC. Post-acquisition, John was appointed Head of Technical Group for LGC Genomics, in charge of all Research & Development and Technical Support activities for the company. In this role John continued to build on the high-quality products and services provided to the companies growing customer base. During the 19 years John has worked in commercial R&D, he has co-invented numerous highly successful products including PACE®, ProbeSure, KASP™, KlearKall, KlearGene, KlearAmp and KlearTaq™, creating breakthrough offerings in genotyping and extraction and generating huge revenues for the companies he has worked in. In 2017, he joined forces with Steve Asquith and started 3CR Bioscience. John is dedicated to developing outstanding, innovative genotyping products and providing the very best technical support to customers globally.
Dr. Nisha JainOperations Director
Nisha has been innovating since the start of her career at Geneform Technologies developing Iso-thermal Genotyping Technologies. Nisha joined KBioscience in 2008, as Senior R&D Scientist and key account Technical Support Scientist, developing KASP and Klearkall performance and coinventing two further versions of KASP. Nisha has more than 15 years’ experience working in molecular biology and genotyping technologies, with extensive experience in the areas of R&D, Quality Assurance and Customer Technical Support. She has technically assisted many giants of the industry with their protocol development and troubleshooting and continues to deliver high-quality support and guidance. In 2018, Nisha joined 3CR Bioscience as Operations Director where she continues to develop PACE and ProbeSure for an increasing range of applications, and to grow 3CR Bioscience’s new product pipeline. Nisha is dedicated to developing outstanding, innovative genotyping products and providing the very best technical support to customers globally.
Nazma Saffin General Manager
For 20 years Nazma Saffin has worked and gained extensive expertise within the genotyping sector. Working at Kbioscience and then LGC, she has held operational leadership posts responsible for manufacturing and laboratory services. With experience of ISO 9001 implementation, production scale up and LEAN operations, Nazma has successfully led highly profitable production departments. Joining 3CR Bioscience in 2022, Nazma is committed to delivering operational excellence.
Jon Curtis Non-Executive Chair
After 8 years in The Royal Air Force, Jon moved to the Imperial Cancer Research Fund where he pioneered the use of ultra high-throughput genomic automation, capable of 46,000 PCRs per hour. In the 1990’s Jon joined GlaxoSmithKline, implementing a high-throughput genomics platform into their drug discovery pipeline. Whilst there he also developed acoustic mixing into compound management, becoming the gold standard across pharma. Jon developed the world’s first commercially viable 1536-well PCR plates, automated thermal & laser plate-sealer, plus automated liquid-handling & tip washing tools to reduce waste and costs. In 2002 Jon co-founded KBioscience with Phil Robinson, utilising ultra high-throughput PCR instrumentation & a suite of automation tools to create the company’s SNPline robotic platform, with a capacity of 250,000 PCRs/day. The business was underpinned by their ground-breaking patented genotyping chemistry, KASP™, which has over 10,000 scientific papers to date. In November 2022 Jon joined 3CR Bioscience acting as an advisor bringing his commercial and scientific experience to the company.