Genomics-led improvement of biotic and abiotic stress tolerance in mustard rape for economic and environmental sustainability

Lead Research Organisation: University of York
Department Name: Biology

Abstract

The proposed research is a Newton-Bhabha development programme. The overall aim is to transfer and optimize UK expertise in genomics, which is the scientific approach involving analysis in parallel of the complete set of genes of an organism, for improvement of both economic and environmental sustainability of mustard rape (Brassica juncea) in India.

The crop characteristics (traits) that are the focus of the research were defined by the Indian partners in the proposal as the most important challenges faced by the crop in India. There are tolerances to the range of environmental challenges (stresses): diseases and infestations from fungi (causing white rust, stem rot, black spot), viruses (Turnip mosaic virus), pests (aphids and butterflies) and root parasites (broomrape) and conditions of high temperatures, drought and salinity. Of particular importance is that multiple stresses are often encountered simultaneously and interactions and trade-offs between tolerance mechanisms can be expected, necessitating an integrated approach across this broad range of challenges. Included in a broad correlation analysis between the traits will be an assessment of associations with variation in classes of chemicals produced by the plants that are recognised as playing roles in tolerance to environmental stresses. To enable this programme to be undertaken thoroughly and successfully, we have assembled a consortium comprising 39 co-applicant scientists representing 17 institutions.

The approach is to establish a toolkit of technologies to help understand the basis of naturally-occurring tolerances and to enable future work to enhance them. These include the establishment of a platform enabling the association of trait variation in panels of genetically diverse mustard rape varieties with variation of both gene sequences and gene activity (expression) to enable the development of molecular markers to accelerate breeding and identify candidate causative genes for further investigation. Non-GM approaches for improvement beyond the range of existing natural variation will be established for mustard rape, including modernised resources for the traditional approaches of radiation breeding and wide crossing with related species, and the emerging technology of genome editing.

Underpinning the programme is the experience gained in developing the Brassica juncea genomic platform currently used by the University of York and University of Delhi South Campus as part of their current Crop Genomics and Technologies (CGAT) project "Broadening the genetic diversity underpinning seed quality and yield related traits in mustard rape and oilseed rape" will be updated to incorporate emerging genome sequences from B. juncea and its progenitor species. The platform will be used to support the trait-focussed activities of the consortium, modelled on the University of York-led "BBSRC Renewable Industrial Products from rapeseed (RIPR) programme". A particular feature will be the highly integrated nature of the research with expertise contributed by world-leaders in the respective components being shared. UK expertise will be transferred to partners in India for application in mustard rape. The benefits of scientific understanding and ability to improve traits in mustard rape accrue primarily to the Indian members of the consortium. However, they will also be of use for improving the corresponding traits in oilseed rape for cultivation in the UK.

Planned Impact

As the largest oil crop in India, mustard rape has the greatest potential to increase oilseed production overall. It fits well in crop rotations systems and has well-established supply chains from breeders to consumers, making it the obvious oilseed choice for PORI. Stress-related losses are huge. For example, 37% estimated for Alternaria blight in combination with white rust (Bal and Kumar, 2014). Small-scale farmers have limited resources to invest in crop protection, making genetic improvement an attractive approach.

We propose to develop knowledge and plant resources that will underpin the predictive breeding of mustard rape with improved agronomic characters promoting economic development in India by increasing the country's own production of edible oils, and doing so sustainably. Initially this will address the most important biotic and abiotic stresses facing the crop in India. However, the platforms and resources established can be used to address the improvement of any trait in mustard rape, leading to very broad impact. The platforms are extendible to other vegetable and seed brassicas, while modern genomic approaches apply to all crops.

Economic development and improved welfare (including their health and education opportunities) at the farmer level comes from improved crops. The genomic underpinning for a major Indian crop presented here will lead directly to new varieties which can disrupt the paradox of farmers (women and men) as primary producers also having the poorest and most disadvantaged families in society. As many Work packages make clear, even 'standing still' in terms of crop production is an enormous challenge. New disease types (biotic stress) are continuously attacking existing crop varieties, while the increasing lack of fresh water and climate change (abiotic stress) threaten current yields, while, population sizes and food requirements are increasing, and cannot be met with the unsustainable options of more land, water, crop protection chemicals and fertilizer. Changing farming practices threaten the environment and the social structure of India. By delivering understanding and approaches with appropriate training and development, our partnership will lead to new, sustainable, resilient and productive mustard rape crop genetics to alleviate the poor yields and quality for Indian smallholders via our Indian partners.

Publications

10 25 50
 
Description Advice to UK Committee on Climate Change
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Title CRIPR transformation of Brassica juncea 
Description Capability to carry out genetic transformation of Brassica juncea 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? Yes  
Impact It is still being used to verify impact on new varieties. 
 
Description Biochemical characterisation of traits potentially involoved in interaction with pests and pathogens in Indian mustard (Brassica juncea) 
Organisation Punjab Aricultural University
Country India 
Sector Academic/University 
PI Contribution Rothamsted Research hosted two visiting Scientists form the Punjab Agricultural University (PAU: Dr Sanjula Sharma and Dr Rimaljeet Kaur) for four months from June to October 2019. Rothamsted research provided accommodation, full access to research facilities and instruments, and training in a wide range of analytical procedures relevant to this Newton Bhabha project (See training outcome below)
Collaborator Contribution PAU provided staff salary and paid for international travel. Visiting Scientist carried out experiments under the supervision of Rothamsted scientists and generated data that will contribute to the success of this project. Typically they conducted biochemical analyses and analysed resistance to fungal pathogens and Aphids using a Brassica juncea diversity panel composed of 50 cultivar and 88 introgression lines.
Impact This collaboration is highly multidisciplinary. During Their stay Dr Sharma and Dr Kaur received training in wide range of experimental procedures ranging from plant cultivation in controlled environment, analytical biochemistry techniques and methods to investigate plant interaction with specific pest insects and fungal pathogens. The analytical methods Dr Sharma and Dr Kaur learned at Rothamsted include: - Cultivation of Brassica Juncea plants in vitro, in CE cabinets and glass house compartments - Extraction of seed oil and total lipids from plant vegetative tissues. - Extraction and derivatisation of plant surface lipids (e.g. cuticular wax) - Analysis of neutrolipid (seed oil and cuticular wax) by Thin Layer Chromatography (TLC) - Preparation of Fatty Acid Methyl Ester (FAMEs) from plant tissue or lipid extracts. - Extraction and derivatisation of seed phytosterol. - Quantitative and Qualitative analysis of FAMEs, wax and phytosterols using Gas Chromatography (GC-FID) and Mass Spectrometry (GC-MS) - GC and MS data extraction, curation, formatting and analysis. - Interpretation of lipid mass spectra and molecular species determination. - Determination of sucrose, glucose and fructose content in plant tissue using an enzymatic methods and light spectroscopy. - Rearing of aphids (Lipaphis erysimi) in controlled environment. - Aphid growth kinetics in vitro using leaf disks to evaluate the relative resistance/susceptibility of B. juncea cultivars. - Inoculation of B. juncea plants with fungal pathogens in GH for evaluation of resistance/sensitivity (e.g. Altenaria and Sclerotinia sp)
Start Year 2019
 
Description Discovery of the genetic basis of partial resistance against Pyrenopeziza brassicae in oilseed rape (Brassica napus) 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Our research team has provided the Principal supervisor and second supervisors for this PhD project. The work is mostly done at the University of Hertfordshire.
Collaborator Contribution Rothamsted Research (Dr Fred Beaudoin) has provided advice and facilities for parts of this project.
Impact The student (Ajisa Ali) has presented the work at UK national (e.g. British Society for Plant Pathology) and international (e.g. Brassica meeting, St Malo, France, July 2018) conferences
Start Year 2018
 
Description Population dynamics of Pyrenopeziza brassicae under Irish field conditions 
Organisation Teagasc
Country Ireland 
Sector Public 
PI Contribution Our University has provided the Principal and second supervisors for this Walsh PhD project (student Diana Bucur). She is doing the research at the Teagasc Oak Park Research Centre at Carlow, Ireland but registered for a PhD at the University of Hertfordshire.
Collaborator Contribution The funding for the project comes from the Walsh Foundation at Teagasc. The day-to-day supervision of the work is provided by Dr Stephen Kildea, a scientist based at Teagasc; they also provide the facilities and consumables for doing the work.
Impact Diana Bucur has presented results from the project at local and international scientific conferences.
Start Year 2019
 
Description Prof Mirinal Maiti 
Organisation Indian Institute of Technology Kharagpur
Country India 
Sector Academic/University 
PI Contribution The training of laboratory staff in CRISPR technique.
Collaborator Contribution Carried out knockouts in the FAE gene of Brassica juncea (Indian Mustard)
Impact Knockout lines are available
Start Year 2019
 
Description The role of oilseed rape leaf wax characteristics in resistance against the light leaf spot pathogen Pyrenopeziza brassicae 
Organisation Chadacre Agricultural Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Our Research Team has provided the Principal Supervisor and second supervisors for this MSc by research project (student Heather Fell). The student is based at the University of Hertfordshire for this work.
Collaborator Contribution Rothamsted Research (Dr Fred Beaudoin) has provided advice and facilities for parts of the work. The three charities have provided funding for the work.
Impact The MSc student has presented the work at UK scientific conferences
Start Year 2019
 
Description The role of oilseed rape leaf wax characteristics in resistance against the light leaf spot pathogen Pyrenopeziza brassicae 
Organisation Felix Cobbold Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Our Research Team has provided the Principal Supervisor and second supervisors for this MSc by research project (student Heather Fell). The student is based at the University of Hertfordshire for this work.
Collaborator Contribution Rothamsted Research (Dr Fred Beaudoin) has provided advice and facilities for parts of the work. The three charities have provided funding for the work.
Impact The MSc student has presented the work at UK scientific conferences
Start Year 2019
 
Description The role of oilseed rape leaf wax characteristics in resistance against the light leaf spot pathogen Pyrenopeziza brassicae 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Our Research Team has provided the Principal Supervisor and second supervisors for this MSc by research project (student Heather Fell). The student is based at the University of Hertfordshire for this work.
Collaborator Contribution Rothamsted Research (Dr Fred Beaudoin) has provided advice and facilities for parts of the work. The three charities have provided funding for the work.
Impact The MSc student has presented the work at UK scientific conferences
Start Year 2019
 
Description Understanding host resistance to improve control of light leaf spot on winter oilseed rape in the UK 
Organisation RSK ADAS Ltd
Country United Kingdom 
Sector Private 
PI Contribution Our team is providing the Principle and second supervisors for this Hertfordshire Knowledge Exchange Partnership PhD project (student Laura Sapelli). The student will spend one year based at ADAS Boxworth before returning to the University to complete the PhD project.
Collaborator Contribution RSK ADAS (industry supervisor Dr Faye Ritchie) is supervising the first year of the project and will continue to attend regular project meetings throughout the project. The Perry Foundation is providing funding (£40000) and will attend meetings annually.
Impact No outputs yet
Start Year 2020
 
Description Understanding interactions between fungal pathogens Leptosphaeria maculans (phoma stem canker) and Pyrenopeziza brassicae (light leaf spot) on Brassica napus (oilseed rape) 
Organisation Chadacre Agricultural Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Our research team has provided the Principal Supervisor and Second Supervisors for this Hertfordshire Knowledge Exchange PhD project . The student (James Fortune) has spent the first year based with ADAS at Boxworth and is now spending the remaining three years doing his PhD at the University of Hertfordshire.
Collaborator Contribution The industry partner RSK ADAS supervised the work done by the student (supervisor Dr Faye Ritchie) and regularly attend project meetings to assess progress of the project. The two agricultural charities have provided funding for the project and attend meetings from time to time.
Impact The student James Fortune has presented work done in this project at several scientific conferences, both in the UK (eg British Society of Plant Pathology conference, Sept 2019) and overseas (International Society of PLant Pathology Congress, Boston, USA, July 2018). His work is also featuring in a book to be published to celebrate the centenary of the Chadacre Agricultural Trust.
Start Year 2017
 
Description Understanding interactions between fungal pathogens Leptosphaeria maculans (phoma stem canker) and Pyrenopeziza brassicae (light leaf spot) on Brassica napus (oilseed rape) 
Organisation Felix Cobbold Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Our research team has provided the Principal Supervisor and Second Supervisors for this Hertfordshire Knowledge Exchange PhD project . The student (James Fortune) has spent the first year based with ADAS at Boxworth and is now spending the remaining three years doing his PhD at the University of Hertfordshire.
Collaborator Contribution The industry partner RSK ADAS supervised the work done by the student (supervisor Dr Faye Ritchie) and regularly attend project meetings to assess progress of the project. The two agricultural charities have provided funding for the project and attend meetings from time to time.
Impact The student James Fortune has presented work done in this project at several scientific conferences, both in the UK (eg British Society of Plant Pathology conference, Sept 2019) and overseas (International Society of PLant Pathology Congress, Boston, USA, July 2018). His work is also featuring in a book to be published to celebrate the centenary of the Chadacre Agricultural Trust.
Start Year 2017
 
Description Understanding interactions between fungal pathogens Leptosphaeria maculans (phoma stem canker) and Pyrenopeziza brassicae (light leaf spot) on Brassica napus (oilseed rape) 
Organisation RSK ADAS Ltd
Country United Kingdom 
Sector Private 
PI Contribution Our research team has provided the Principal Supervisor and Second Supervisors for this Hertfordshire Knowledge Exchange PhD project . The student (James Fortune) has spent the first year based with ADAS at Boxworth and is now spending the remaining three years doing his PhD at the University of Hertfordshire.
Collaborator Contribution The industry partner RSK ADAS supervised the work done by the student (supervisor Dr Faye Ritchie) and regularly attend project meetings to assess progress of the project. The two agricultural charities have provided funding for the project and attend meetings from time to time.
Impact The student James Fortune has presented work done in this project at several scientific conferences, both in the UK (eg British Society of Plant Pathology conference, Sept 2019) and overseas (International Society of PLant Pathology Congress, Boston, USA, July 2018). His work is also featuring in a book to be published to celebrate the centenary of the Chadacre Agricultural Trust.
Start Year 2017
 
Description 15th International Rapeseed Congress 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Poster presentation # 535 at 15th International Rapeseed Congress from 16th to 19th June 2019 in Berlin: Understanding the genetic and molecular basis of tolerance to sclerotinia stem rot (SSR) and alternaria black spot (ABS) in Brassica juncea by Haitham Sayed, Jon S. West, Bruce D. L. Fitt and Henrik U. Stotz.
Met Indian colleagues on the project: Pankaj Sharma from DRMR and Prabhjodh Singh Sandhu and colleagues from PAU.
Year(s) Of Engagement Activity 2019
 
Description British Society for Plant Pathology Presidential Meeting, Bristol, Sept 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The BSPP presidential meeting was attended by a group of staff/students from the University of Hertfordshire. The event provided an opportunity to present our work as oral presentations and posters. It also gave opportunities to interact with collaborators.
Year(s) Of Engagement Activity 2019
URL https://www.bspp.org.uk/conferences/arms-race-evolution-of-plant-pathogens-and-their-hosts/
 
Description British Society for Plant Pathology meeting from 2nd to 3rd September 2019 in Bristol 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact BSPP meeting from 2nd to 3rd September 2019 in Bristol; poster presentation: Understanding the genetic and molecular basis of tolerance to sclerotinia stem rot (SSR) and alternaria black spot (ABS) in Brassica juncea by Haitham Sayed, Jon S. West, Bruce D. L. Fitt and Henrik U. Stotz.

Sponsored and met Indian colleague on the project Navin Gupta from National Research Centre on Plant Biotechnology, New Delhi.
Year(s) Of Engagement Activity 2019
 
Description GCIRC 15th International Rapeseed Congress, Berlin, June 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A group of staff/post-graduate students from the University of Hertfordshire attended this Congress and accompanying workshops. Our work was presented as oral presentations and posters. There were opportunities to interact with collaborators from around the world. I was part of the International Organising Committee and am a UK representative on GCIRC Council.
Year(s) Of Engagement Activity 2019
URL https://www.irc2019-berlin.com/
 
Description UKRI-UP-SIGN GCRF workshop 30th April & 1st May 2019, Swansea University 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The event was a workshop to connect potential UK and Pakistan collaborators and to plan consortia for future GCRF funding calls
Year(s) Of Engagement Activity 2019