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.
