Controlling dormancy and sprouting in potato and onion

Lead Research Organisation: Cranfield University
Department Name: School of Water, Energy and Environment

Abstract

Potato and onion are major UK and worldwide crops required year-round by consumers and processors. Due to seasonal production, long term storage is necessary, during which produce must be maintained with good quality for fresh consumption and processing, and in a nutritious state. Potato tubers and onion bulbs are natural over-wintering structures with a tendency to resume growth during storage, resulting in sprouted produce that is unattractive and unsaleable, or unsuited to processing due to compositional changes such as increased sugar levels. Multiple strategies are used to extend dormancy and minimise sprouting and waste, including low temperature storage and application of sprout suppressants such as chlorpropham, maleic hydrazide or ethylene. Such treatments are not fully effective as quality deterioration may occur even if sprouting is inhibited and legislation increasingly limits use of many of these chemicals. In addition, long-term cold storage is a major economic cost with a substantial carbon footprint.

Development of alternative strategies to maintain tubers and bulbs in a dormant state and long-term suppression of sprouting are top industry priorities. Genetic studies in potato have shown that inheritance of tuber dormancy characteristics is affected by several genes acting alone or in combination, but the identity of these genes is unknown. Despite substantial progress, a full understanding of the biology of dormancy and sprouting has not yet emerged, and this substantially hampers development of new strategies for storage, and breeding of new varieties with better dormancy and sprouting behaviours. Fortunately recent advances in the field of molecular biology allow us to make major advances to address these issues.

Scientific studies have revealed common roles in potato and onion for several plant hormones including abscisic acid, ethylene, gibberellins and cytokinins, in regulation of dormancy, and sprout growth, suggesting that knowledge of one commodity further our understanding of another. This project will benefit from major advances in potato genetics, especially publication of the genome sequence, as well as huge developments in DNA sequencing technologies which now enable in-depth analysis of the relatively unexplored but highly complex onion genome. New, powerful potato genetic resources will allow us to pinpoint the position and identity of genes that exert the greatest control of dormancy and sprouting. These resources include large mapping populations, developed by crossing highly divergent parents. Preliminary studies have already revealed genomic regions containing key genes that can drive crop improvement and new management methods.

The assembled research consortium brings together James Hutton Institute, Cranfield University, Imperial College London and Greenwich University, providing a wealth of experience in genomics, genetics, molecular biology, physiology, agronomy and storage of potato and onion.

Project outcomes will include (1) identification of key genes in potato and onion, their variant forms and regulatory mechanisms that underpin potato tuber dormancy, (2) development of genome-wide data on major genes in onion bulb dormancy and sprouting, and (3) comparison of shared and distinctive elements of dormancy and sprouting control in potato and onion, leading to elucidation of key physiological and molecular control steps.

Through involvement of industry representative bodies and companies, information generated can readily be translated towards enhanced, variety-specific storage regimes, enabling reduced chemical usage and less reliance on expensive low temperature storage. Knowledge of key regulatory genes can in the longer term be adopted by breeders to develop potatoes with better dormancy characteristics.

Technical Summary

This science-led project addresses a major commercial problem in potato and onion industries, namely loss of crop value and quality due to untimely postharvest sprouting from tubers and bulbs. Chemical controls are widely deployed but many of these may be withdrawn and others are not universally effective. Alternative routes to preventing sprouting are therefore urgently needed. Duration of meristem endodormancy and subsequent rate of sprout extension are key traits for which substantial genotypic variation exists, and some of this has been associated with QTLs in potato. However, the underlying genes are not yet defined, nor is the substantial influence of pre- and post-harvest environment fully understood.

We have therefore assembled a team with complementary expertise across genetics, molecular biology, physiology and storage of both species. We will take advantage of unique potato genetic resources, especially substantial mapping populations with diversity in dormancy, and the recent availability of a high quality genome sequence. Onion genomics are much less advanced, but we will access the latest resources and generate novel RNAseq data. This will allow innovative species and genotype comparisons

Our starting point is a working model of hormone signalling in regulation of dormancy and post-dormancy growth; this is based on our data for cytokinins, strigolactones, ethylene and ABA. We will advance and test this model by sampling extreme genotypes from both narrow genetic bases (individuals from mapping populations) and broader potato and onion diversity. By accurately defining duration of endodormancy and tracing transcript and hormone profiles in tuber and meristem tissues throughout crop development and post-harvest storage, we will extract the strongest variables that robustly correlate with, predict and/or regulate dormancy status. Close alignment with industry will enable translation and further testing of models under commercial conditions.

Planned Impact

Who might benefit from this research?
This proposal has been developed in consultation with key UK industrial beneficiaries. Enhanced knowledge and tools relating to potato storage will benefit all industry sectors, reflected by the financial support of the Potato Council, who include this topic as a priority area in their R&D strategy. Direct beneficiaries include PepsiCo PLC, a global company with substantial activity in the UK processing potato market, and Albert Bartlett, UK's leading grower and packer of potatoes (25% market share of UK fresh & seed potato production) Collectively the levy board and industrial partners have committed significant funding to the project (10% cash).

Ultimately project outcomes will impact on sustainable food production. UK food self-sufficiency will result in reduced imports and costs to consumers. In the global economy, improved human nutrition anywhere will improve global security and thereby benefit the UK. Outcomes of this research will also impact on breeding in developing countries. For example the International Potato Centre (CIP) operates several breeding programmes for Asia and Africa, where crop storage facilities are limited. A unified model of dormancy control across crops included here will provide impetus for research on less studied staples (yam, sweet potato) vital for food security in some of world's poorest regions.

How might they benefit from this research?
Currently in the UK, storage waste for potatoes and onions is between 3-25%. Much of this waste is related to breaking of endormancy and premature sprouting. Chemical inhibitors of sprouting (e.g. chlorpropham (CIPC) and maleic hydrazide (MH)) are UK industry standards; however they are under severe threat of being withdrawn under EU regulation, since they are increasingly considered undesirable by consumers and regulators. Currently, of the 4.05 million tonnes of potatoes stored annually in the UK, 44% is treated with CIPC, so there is an urgent need to develop new storage strategies for potato and onion, less reliant on CIPC (please see letter of support from CIPC stewardship group). This new consortium will employ cutting-edge technologies to develop genetic, molecular, biochemical markers in potato and onion for evaluation of dormancy status in existing and emerging cultivars and to understand the impact of agronomic/storage practices on the development of dormancy.

For onion, our proposed research and assemblies will feed directly into the current international efforts on transcriptome analysis for onion and other alliums. With the assistance of Prof. Havey of the University of Wisconsin we will ensure that we integrate and make public onion transcriptome data.

Longer term, plant breeding is the route through which almost all genetic advances in crop production will benefit the wider community. The commercial arm of JHI, Mylnefield Research Services, runs potato breeding programmes for all major UK potato producers, enabling ready routes to translate research outcomes to industry.

Wide dissemination will ensure full benefit of project outcomes. Participation of the Potato Council in the consortium is pivotal through its links across the UK potato industry. The Potato Council will also provide feedback from industry on the project and the uptake of its outcomes. Similarly, established links between CU and the British Onion Producers Association will provide a route to interaction with the onion industry.

NRI-UoG works closely with international research organisations including CGIAR centres such as CIP, IITA and CIAT to support research on root crops in order to improve food security worldwide. It is therefore well placed to ensure that project outputs are fully exploited through breeding and technology development to improve storage and reduce losses for potato, onion and other root crops.

Publications

10 25 50
 
Description This project is aimed at unravelling genetic and molecular processes underlying the very important traits, tuber and bulb dormancy in potato and onion respectively. We have made significant progress in gaining a better understanding of the genetics of tuber dormancy in potato using a diploid cross that shows a high level of variation in the trait. We have detected significant genetic effects on four potato chromosomes and we believe we have identified a good candidate gene for one of these. This is currently being confirmed using transgenic approaches. Other potato work is looking gene expression and other changes (plant growth regulators, hormones etc) in extreme lines from the crossing population. The onion work does not involve genetic analysis so is more focused on a transcriptomic and biochemical approach.

Work has been published and has shown the following thus far:
potato: 1) discovered mechanism to how ethylene can extend eco-dormancy in potato [papers in preparation], 2) discovered a gene family which controls sprout growth/vigour in potato tubers [Morris et al., 2018]
onion: 1) created first de novo transcriptome for onion [paper in preparation] 2) discovered that ethylene can extend eco-dormancy in onion bulbs [paper in preparation], 3) discovered that Fructans redistribution could be used as a predictive marker for onion dormancy-break [Ohanenye et al., 2019]

Other research is covered by a NDA between parties and thus more detailed information cannot be disclosed at this time pending a patent search.
Exploitation Route potato:
1) discovered mechanism to how ethylene can extend eco-dormancy in potato - this could be used by others in industry to improve storage
2) discovered a gene family which controls sprout growth/vigour in potato tubers [Morris et al., 2018] - this could be used by others in industry to improve storage
onion:
1) created first de novo transcriptome for onion - this can be used by other researchers for future onion research
2) discovered that ethylene can extend eco-dormancy and reduce sprout growth in onion bulbs - this could be used by others in industry to improve storage
3) discovered that Fructans redistribution could be used as a predictive marker for onion dormancy-break [Ohanenye et al., 2019] - this could be used by others in industry to improve storage prediction and thus storage scheduling and release
4) The effect of ethylene supplementation on dormancy break and sprout growth resulted in the alteration of the balance in plant growth regulators (abscisic acid and cytokinins) at time to dormancy break, and impacted on their spatial distribution in onion tissue (including auxins) .
Other research is covered by a Master Service Agreement between parties and thus information cannot be disclosed at this time pending a patent search.
Sectors Agriculture, Food and Drink

 
Description Several meetings have been held with industrial partners, notably at Bartletts in Airdrie (2016, 2017), as well as a joint event with Bartletts, Pepsico and AHDB (2016). Various ways are being discussed for industrial partners to make use of results from the project. The main opportunities under discussion are; How to exploit QTL information for dormancy/sprouting in potato to develop markers for breeding; the potential to exploit natural variants in dormancy related candidate genes identified; and investigating the profiles of gene expression, hormone levels and metabolite changes to develop markers for status of potato tubers and onion bulbs in storage. CU (PI Prof. Leon A. Terry) has been awarded a BBSRC grant ("Implementing novel, cost effective alternatives to CIPC for sustainable potato storage" [Reference: BB/M027295/1] which builds upon this project. It aims at developing novel, cost effective, benign, physiologically-targeted storage interventions which will suppress sprouting and maintain low sugars, offering a route to incremental reduction in and ultimately the removal of the use of CIPC in the UK and beyond. Presentations have been given at various crop storage and other events since the inception of the project in 2013, including British Potato 2015 and Potatoes in Practice (2017). A report fro AHDB is in preparation as are other publications on the genetics of dormancy and tuberisation in potato. The research has helped secure additional research funding from the Agritech Catalyst [with Match funding from PepsiCo]. The research has also led to two patent applications and substantive direct from PepsiCo [e.g. fully funded PhD student - details cannot be disclosed due to confidentiality]. The research has also helped to secure a further extension to the Master Service Agreement between Cranfield and PepsiCo.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Implementing novel, cost effective alternatives to CIPC for sustainable potato storage
Amount £525,000 (GBP)
Funding ID BB/M027295/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2015 
End 08/2019
 
Title Detailed potato phenotyping for bud assessment 
Description A detailed phenotyping key (including dormant, pre- eye movement, eye movement/dormancy break, small sprout, and sprout) for potato bud assessment was developed. The assessment had to be done under stereomicroscope and bud samples where further excised for biochemical (viz. phytohormones) and molecular analysis. Such analysis also confirmed the robustness of the protocol for sample extraction, which has been used in two consecutive years within the project. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2018 
Provided To Others? Yes  
Impact The developed methodology was consistently used during the project and further extended to related projects. 
 
Description PepsiCo 
Organisation PepsiCo
Country United States 
Sector Private 
PI Contribution Master Service Agreement signed and renewed [confidential]
Collaborator Contribution Master Service Agreement signed and renewed [confidential]
Impact Master Service Agreement signed and renewed 2 patents Additional research commissioned [e.g. fully funded PhD and contract research] Members of Cranfield staff now working at PepsiCo [Dr Gemma Chope and Dr Kate Cools]
Start Year 2013
 
Description Innovate UK - Knowledge Transfer Network event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was an Invited speaker at BP2017, as part of Innovate UK - Knowledge Transfer Network event, in Harrogate. The aim and objectives, as well as the main findings of the BBSRC funded project 'Controlling Potato Dormancy' Horticulture and Potato Initiative were disseminated as two oral presentations on 22nd and 23rd November, 2017, respectively. Apart from the questions from the audience, separate conversations and further contacts were made with relevant companies from the sector, such as KP Snacks and TOMRA sensors
Year(s) Of Engagement Activity 2017
 
Description Oral presentation on the HaPI dissemination event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Around 80 people attended the event, including industrialists, academics, and researchers. The presentation of the project aim and the main findings that far, as well as the expected impact for UK potato and onion industries (viz. breeders, growers, agronomists) raised interesting questions and debate afterwards.
Year(s) Of Engagement Activity 2016