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

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.

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.