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PACE SNP Genotyping Boosts Hop Breeding with an Affordable & Convenient Diagnostic Marker to Identify Male and Female Hop Plants

SNP Genotyping pushes modern breeding of hops for brewing and beyond

In hop cultivation, identifying female plants is crucial for efficient production. Traditionally, determining a plant’s sex has been a time consuming, extending breeding program by 1-2 years. A recent breakthrough from researchers from the National Clonal Germplasm Repository, OR and Forage Seed and Cereal Research Unit, WA of the USDA-ARS, in collaboration with the University of Minnesota and Hudson Alpha Institute for Biotechnology has generated a cost-effective and convenient SNP genotyping marker using PACE technology.

To develop this, Dr Shaun Clare, Dr Kayla Altendorf and colleagues collaborated to assemble a diverse collection of 765 hop genotypes and conducted Genome-Wide Association Studies (GWAS) on 20,681 bi-allelic SNPs. A highly significant SNP marker on the sex chromosome, accurately predicting sex with 96% accuracy, was discovered.

 

High-throughput SNP genotyping workflow

The teams combined a PACE SNP genotyping assay with targeted allele-specific primers, and a quick DNA extraction methodology for a rapid, high-throughput SNP genotyping workflow. Validation in a separate population achieved 96% accuracy in identifying male and female seedlings. Applied in the USDA-ARS hop breeding program, this marker increased the female-to-male seedling ratio by 25%, resulting in a 97.4% female yard in 2023.

This marker and methodology is widely applicable, requiring only standard molecular laboratory equipment, affordable reagents and saves time, labour, and space, enhancing breeding program planning and efficiency.

This new diagnostic, accurate, affordable, and scalable SNP genotyping marker, applied using PACE technology is a boost for hop breeding and showcases the efficacy of Marker-Assisted-Selection (MAS) techniques for hop breeding.

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SNP Genotyping boosts hop breeding
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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.