Plant Genomics: Breeding More Resilient Tomato Crops

Identifying Candidate Genes and Validating Markers for Anthracnose Resistance Through QTL Analysis and PACE PCR Genotyping.

In a study published last month in Frontiers in Plant Science, researchers from West Virginia State University and The Genetic Improvement for Fruits and Vegetables Laboratory, USDA successfully identified 20 genomic regions linked to anthracnose resistance and identified 24 potential SNP markers for disease resistance, all validated through PACE® Allele-specific PCR genotyping assays. The efficacy of these PACE assay markers holds substantial promise for marker-assisted selection in tomato improvement breeding programs, especially for anthracnose resistance.

Anthracnose, caused by the fungal pathogen Colletotrichum spp., is one of the most significant tomato diseases in the US and worldwide. Currently, no commercial cultivars with anthracnose resistance are available, which limits the potential for resistance breeding. Cultivars with genetic resistance could significantly reduce crop losses, decrease the need for fungicides, and mitigate risks associated with chemical application.

Efforts to transfer disease from landrace collections into elite materials have so far been unsuccessful due to its complex genetic inheritance. Moreover, little is known about anthracnose resistance Quantitative Trait Loci (QTLs) and genomic regions housing them, which has hindered the development of marker assays for high-throughput screening – until now.

Methods in More Detail

A recombinant inbred line (RIL) mapping population (N=243) was made by crossing a susceptible cultivar and a resistant but semiwild, small-fruited cultivar to identify QTLs associated with anthracnose resistance.

The RIL population was assessed for resistance by inoculating ripe field-harvested tomato fruits with Colletotrichum coccodes over two growing seasons. RIL samples were genotyped using genotyping-by-sequencing (GBS) technology and then compared with a reference strain to identify variants. These variants were subsequently used for conventional QTL mapping and GWAS analysis. QTLs were found in several known disease resistant genes.

QTLseq analysis was performed using deep sequencing of resistant and susceptible bulks, which validated the QTL positions identified using traditional mapping and pinpointed candidate genes associated with various QTLs. Closely linked SNPs and QTLs were identified for the target trait in each bulk. A total of 24 potential SNP markers were validated with Allele-specific PACE PCR genotyping assays. Additionally, some of the traits mapped may also serve as candidates for a genome editing approach to engineer anthracnose resistance in tomatoes.

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Plant genomics in tomato crops
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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.