Advancing genomics to enable anticipatory breeding of resistance in brassica crops to diseases of global importance

Lead Research Organisation: University of Warwick
Department Name: School of Life Sciences

Abstract

Brassica juncea (oilseed mustard) is an important multi-purpose crop for the economy and health of people living throughout south Asia. This is particually true in India, where the £ 2.4 billion annual revenue in production is largely cultivated by resource poor farmers in smallholdings of one hectare or less. White blister rust (caused by Albugo candida) is a significant economic problem in developing countries like India where it can cause between 30-60% yield losses in Indian mustard production. Breeding for resistance is the most efficient, cost-effective and environmentally sustainable way of protecting brassica plants from white rust disease. Due to the potential for rapid evolution in A. candida, it is important to identify many independent alleles of white rust resistance (WRR), that when assembled together in the same cultivar could provide broad spectrum disease control. This aim provides the basis for three specific objectives research in the PhD project:
1) Development of a fast-track method for mapping of white rust resistance genes directly from Gene bank collections. This proof-of-concept approach has the potential to map large numbers of WRR alleles from a relatively untapped gene pool in the B.rapa (A-genome). These will then be directly relevant to the amphidiploid B. juncea (AB genome).
2) Molecular investigation of a predicted non-NLR determinant of white rust incompatibility. CRISPR-CAS9 will be used for loss-of-function testing of a candidate GDSL Lipase that require validating for effects on altered WR suceptibility. If none is evident then further experiments will need to be designed to define the acting gene.
3) Development of pathogenomics to aid selection of complementary R-alleles for 'gene-stacking'. This work will further understanding of pathogen population structures as well as identifying candidate AVR elicitors that correspond to resistance genes in B. juncea and/or B. rapa cultivars.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M01116X/1 01/10/2015 30/09/2023
1782601 Studentship BB/M01116X/1 03/10/2016 30/09/2020 William Crowther
 
Description We have now demonstrated a highly efficient method for rapidly mapping novel resistance (white rust resistance) loci, directly from undeveloped Gene bank germplasm. This was accomplished using a combination of whole genome sequencing and bulked segregant analysis to generate multiple QTL regions across 5 distinct B.rapa landraces. Screening was performed using a UK race 2 A.candida isolate - AcBj12, which has been shown to break the recently discovered and main WRR gene (BjuWRR1) in Indian Mustard (B.juncea). Resistance loci discovered here are of direct relevance therefore to both B.rapa and B.juncea production.

A QTL locus on chromosome 2 was mapped in the same local region for AcBj12, and also AcBjDC - a second BjuWRR1 virulent race 2 isolate. This suggests that the same mapped gene is likely responsible for resistance to both isolates. We have explored sequence within this QTL to identify 8 classical NB-LRR resistance candidates, 6 of which have distinct alleles that associate to phenotype. The resistant alleles for these genes are currently being cloned into a susceptible Arabidopsis background for functional testing. This experiment provides provides a useful demonstration of how quickly one can go from germplasm to functional testing of candidate genes, a process that typically takes a few years.

We are also working to generate long-read nanopore assemblies for the two isolates AcBj12 and AcBjDC. This will provide improvements to current assemblies, and will also provide useful documentation of their effector gene repertoires.
Exploitation Route Genes mapped in this study would be directly of use to breeding efforts for durable WR resistance in Indian cultivars of B.Juncea that are predominantly grown by resource-poor farmers.
Sectors Agriculture, Food and Drink,Environment

 
Description Establishing an India-Africa-UK innovation hub for seed and root health in brassica and bean crops
Amount £23,516 (GBP)
Funding ID BB/GCRF-IAA/17/22 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 02/2018