Low cost DNA identification of crop varieties

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

Wheat is the world's most widely grown commercial crop in terms of land area and yield and supplies 19% of all calories consumed. Global annual production is around 0.7 billion tonnes with a total export value of $46 billion. In the UK, wheat is the most important crop by yield at 15 million tonnes. Compared to other cereals, wheat lacks the genetic diversity required for resilience and yield increases in line with global demands. Unless germplasm diversity is managed with great care and coordination, selective breeding inevitably reduce diversity further over time. Efforts to direct elite variety crosses within the breeding industry and progress these rapidly to market are undermined by a complete lack of standardised varietal identification system, not just globally but even within the UK academic and breeding communities, leading to misidentifications within germplasm collections and a lack of interoperability between and among breeders, academics and regulators, all of whom use different genetic markers or none at all. In this proposal we will engage the international wheat community through the coordination umbrella of the Wheat Initiative, the UK breeding sector - via our partners at RAGT, and DSV and the regulatory framework of the British Society of Plant breeders to test and deploy an optimal set of genetic markers capable of discriminating wheat and other crop varieties at low cost. BBSRC funding over the past 20 years has brought us to the point where we have been able to screen thousands of hexaploid wheat lines with over 35,000 genetic markers. We have developed an algorithm that was able to select just 29 markers from these data that were able to discriminate all 2040 lines. In this project we will convert these markers to low cost KASP assays for use in industry and academia. The inclusion of the national and globally significant seed repository for wheat - the GRU at the John Innes Centre in addition to the majority of European breeding companies ensures that we can set the benchmark for genetic markers for wheat and lead by example globally. Our website, http://www.cerealsdb.uk.net which has been a key international repository for wheat genotyping data since 2004 will be used to disseminate the marker data and host a web tool for identifying varieties genotyped with our panel. The marker system will be made freely available and we anticipate primary impact through its widespread adoption as a standard system run in-house by breeders and academics. We will also offer this as a service at a total cost of £10 per sample (including DNA extraction) through our well-established Bristol Genomics Facility on a non-profit full economic cost basis.

Publications

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Burridge AJ (2024) Development of a next generation SNP genotyping array for wheat. in Plant biotechnology journal

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Burridge, A.J. (2024) Development of a Next Generation SNP Genotyping Array for Wheat in Plant Biotechnology Journal

 
Description The minimal marker development approach funded proved to be useful in an unexpected way. Whilst the genetic marker system we trialled proved to have a higher failed call rate than expected, we were able to use the approach to optimise the selection of genetic markers across the wheat genome. We used this approach to develop a whole genome genotyping chip in collaboration with Thermo Fisher and the Agricultural Genomics Institute Shenzen among others.
This new chip has been released to the community for purchase.
Exploitation Route Academics and breeders have access to a greatly improved and optimised genotyping system for wheat and a published and reproducible method for developing such systems for other crops.
Sectors Agriculture

Food and Drink

 
Description The algorithm we developed for selecting a set of minimal genetic markers required for identifying a crop variety was the basis for this follow-on funding. We found that a major additional application of this algorithm was the selection of genetic markers optimised for delineating haplotype blocks within wheat chromosomes. We applied this to develop a novel wheat genotyping Axiom array with commercial partner, Thermo Fisher Ltd. This array is being tested and is due for public release in April 2023. Update: The array was released commercially in late 2023 and a publication on its development accepted for publication. It is now in use by multiple academic and industry users.
First Year Of Impact 2024
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BBSRC Institute Strategic Programme: Delivering Sustainable Wheat (DSW) Partner Grant
Amount £699,772 (GBP)
Funding ID BB/Y003004/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2023 
End 03/2028
 
Description Bristol Center for Agricultural Innovation
Amount £20,384 (GBP)
Funding ID A Next Generation Genotyping Array 
Organisation University of Bristol 
Department School of Biological Sciences
Sector Academic/University
Country United Kingdom
Start 03/2021 
End 03/2022
 
Description Generation of a novel 35K Axiom genotyping array from AGIS skim sequence data 
Organisation Agricultural Genomics Institute at Shenzhen
Country China 
Sector Public 
PI Contribution We have collaborated with AGIS by using our minimal marker software to scan through over 900 wheat skim sequenced genomes and generate 35,000 uncorrelated and evenly spread SNP markers for a new, commercial, Axiom genotyping chip.
Collaborator Contribution AGIS shared access to over 900 sequenced and SNP called wheat varieties
Impact A novel genotyping axiom array has been manufactured and will be available to the public (academics and wheat breeders) as soon as in-house quality control has been completed.
Start Year 2021
 
Description A New Genotyping Array for the Next Generation of Wheat Breeding: Presentation at Thermo Fisher workshop, International Plant and Animal Genomics Meeting, San Diego 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Using the software approach to marker selection that forms the basis of this follow-on fund, we developed a haplotype-optimised wheat genotyping array in collaboration with Thermo Fisher. We presented the new array and explained our novel approach to the selection of markers for haplotype optimisation in this presentation.
Year(s) Of Engagement Activity 2023
URL https://www.thermofisher.com/uk/en/home/about-us/events/life-science/pag.html
 
Description MONOGRAM 2021 conference presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The minimal marker approach to identify a set of markers for wheat varietal ID was presented to the MONOGRAM network meeting on the 1st of June. The conference has the key academic and industry stakeholders (UK and European breeding companies) in attendance.
Year(s) Of Engagement Activity 2021
URL https://www.conventiondundeeandangus.co.uk/uploads/tinymce/TD/Conference%20Programme%20&%20Abstract%...
 
Description Oral presentation at the 2024 International Plant and Animal Genomics Meeting, San Diego 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A presentation was made on the use of our minimal marker selection algorithm for the optimisation of a novel wheat genotyping system. The audience consisted of around 200 academics and plant breeding industry researchers. Follow up meetings were help with researchers at overseas Universities and European plant breeding companies.
Year(s) Of Engagement Activity 2024
URL https://pag.confex.com/pag/31/meetingapp.cgi/Paper/54269
 
Description Poster PO0283 A Low-Cost Genotyping Approach to Identification of Apple Cultivars- presented at the International Plant and Animal Genomics Meeting, San Diego Jan 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster abstract:
The accurate identification of accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. We describe here an inexpensive, reliable, and rapid genotyping method which can be used in any season at any growth stage and avoids the need for laborious and time-consuming morphological comparisons.

Single Nucleotide Polymorphism (SNP) marker panels have been developed for many crop species, but, being designed for research, they have far more markers than would be required for varietal identification and are too expensive to use for routine cultivar identification.

Using a novel marker optimisation method designed to select only highly informative SNPs, we have designed a minimal panel of SNP markers, consisting of only 21 markers, that is sufficient to distinguish all distinct apple cultivars held in the English and Welsh National Collection. We show that SNP genotyping with a small set of well selected SNP markers is as efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.
Year(s) Of Engagement Activity 2023
URL https://plan.core-apps.com/pag_2023/abstract/963d7d6c9252da3647857a6b5d04fe6c