Accelerated breeding of black rot resistant brassicas for the benefit of east African smallholders
Lead Research Organisation:
Harper Adams University
Department Name: Agriculture and Environment
Abstract
Plant disease resistance genes can protect crops against pathogens that have the corresponding avirulence (avr) genes. In many cases, the protection conferred by single, generally dominant, disease resistance (R) genes is short lived as the pathogen strains can evolve through mutation and selection, favouring strains with altered or missing avr genes that are therefore able to cause disease. Broad spectrum disease resistance that is quantitative, involving several genes, is generally expected to be more durable. However, this kind of resistance is more difficult to exploit in breeding programmes. The basis of this plant defence strategy is currently unknown. We have chosen quantitative resistance to Xanthomonas campestris pv campestris (Xcc) in Brassica rapa as a model for investigation. Xcc causes black rot of crucifers. This seed-borne disease is one of the most important diseases of Brassicas worldwide. In previous Brassica research at WHRI we have identified good sources of resistance and mapped the location of the major genetic components. In this project we will exploit the exciting new developments in Brassica rapa genomics and emerging information on the close relatedness of the Brassica and Arabidopsis genomes to characterise the resistance and identify the genes involved. The combination of the above resources in the proposed project will allow us to deliver novel and exciting information on the fundamental basis of quantitative disease resistance in a crop species. Key practical outcomes of this work will be resistant plant material with tightly linked molecular markers and information on the extent of natural variation for resistance in Brassica genomes that could be exploited in plant breeding to provide durable resistance to a very significant pathogen.
Technical Summary
This multidisciplinary project will combine expertise in genetics, breeding, genomics and pathology to generate novel information on quantitative resistance to black rot caused by Xanthomonas campestris pv. campestris, a major disease of Brassicas. Quantitative resistance, involving the cumulative phenotype expressed by numerous genes, is generally expected to be more durable than resistance due to single dominant genes. However, this kind of resistance is more difficult to exploit in breeding programmes. We will dissect the resistance in Brassica rapa into major components and determine their relative contribution. We will utilise new developments in B. rapa genomics and emerging information on synteny between the Brassica and Arabidopsis genomes to fine-map and identify the genes involved. The spectrum of the resistance will be determined against a wide range of pathogen isolates from our culture collection. Representative sets of the Brassica genepool will be screened to identify allelic variation and potential new candidates for resistance breeding. Well defined resistant germplasm with tightly linked molecular markers and information on allelic variation in Brassica genomes will be key practical outcomes. Specific objectives of this study are: 1. Characterisation of the major components of quantitative Xanthomonas campestris pv. campestris (Xcc) race 1 and race 4 resistance from Brassica rapa; 2. Fine-scale mapping to identify closely linked markers and candidate genes using synteny between the Arabidopsis and Brassica genomes. 3. Clone candidate genes and transform into B. oleracea for functional testing in a C genome recipient. 4. Assess the broad spectrum potential of the B. rapa resistance for protection against a range of Xcc isolates. 5. Survey allelic variation for resistance loci in other Brassica genomes using Brassica Differential Fixed Foundation Sets (DFFS)
Organisations
Publications
Mulema J
(2011)
Characterization of isolates that cause black rot of crucifers in East Africa
in European Journal of Plant Pathology
Vicente JG
(2013)
Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops.
in Molecular plant pathology
Description | 1. New information on the distribution and molecular characterisation of Xcc in East Africa was produced. Incorporation of the Xcc data into the CABI Plantwise database will assist plant breeders in choosing suitable germplasm and targets for resistance breeding, and provide information to extension specialists advising farmers on suitable Brassica cultivars for planting. 2. Further characterisation of Xcc resistance in brassica confirmed that it is absent or rare across a wide representative sample of the C genome and showed that the resistance in B. rapa is broad-spectrum and robust against a range of Xcc isolates, reinforcing it's potential for resistance breeding. 3. The capacity building grant provided training and resources to significantly improve the capability of KARI pathologists to identify and characterise Xcc and the opportunity to develop further research links in this area. |
Exploitation Route | Incorporation of the Xcc data into the CABI Plantwise database will assist plant breeders in choosing suitable germplasm and targets for resistance breeding, and provide information to extension specialists advising farmers on suitable Brassica cultivars for planting. 3. The capacity building grant provided training and resources to significantly improve the capability of KARI pathologists to identify and characterise Xcc and the opportunity to develop further research links in this area. |
Sectors | Agriculture Food and Drink |
Title | Culture collection of Xcc isolates from E. Africa |
Description | A set of 249 new Xcc isolates collected from East Africa for this project have been added to the Xcc culture collection at Warwick. A subset which are representative of the pathotype and genetic diversity have been sent to the project partners in Kenya. |
Type Of Material | Biological samples |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | This collection (and the associated database described elsewhere) greatly extends information on the distribution of races of this important bacterial pathogen in E. Africa. It has been shared with project partners in Kenya for use by pathologists, breeders, growers and other researchers. |
Title | DNA sequences of Xcc genes involved in pathogenicity |
Description | 97 DNA sequences for Xcc gyraseB genes have been deposited in the NCBI under GenBank accession numbers HQ200306-HQ200403. 94 DNA sequences for Xcc AvrXccC genes have been deposited in NCBI under GenBank accession numbers HQ169543- HQ169637. 89 DNA sequences for Xcc xopXccN genes have been deposited in NCBI under GenBank accession numbers JF312229- JF312318. These sequences will aid in studies of molecular pathology and genetic diversity of Xanthomonas spp. in Africa and elsewhere. |
Type Of Material | Biological samples |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | These sequences will aid in studies of molecular pathology and genetic diversity of Xanthomonas spp. in Africa and elsewhere. |
Title | B. rapa SNP database |
Description | A panel of 1556 Brassica SNPs generated from transcriptome sequence of the B. rapa mapping parents during this project will be made publicly available through the Defra VeGIN website. |
Type Of Material | Database/Collection of data |
Year Produced | 2013 |
Provided To Others? | Yes |
Impact | Increased density of polymorphic SNP markers on the Brassica rapa genetic map for use by researchers and breeders. |
URL | http://www2.warwick.ac.uk/fac/sci/lifesci/research/vegin/ |
Title | Database of Xcc isolates from East Africa |
Description | A database of the geographical source, host plant and characterisation data for 249 Xcc isolates collected from East Africa during this project is available and this has been passed to CABI partners for incorporation into the CABI Plantwise initiative knowledge bank. |
Type Of Material | Database/Collection of data |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | Incorporation of the Xcc data into the CABI Plantwise database will assist plant breeders in choosing suitable germplasm and targets for resistance breeding, and provide information on regional distribution of races of the pathogen to extension specialists advising farmers on suitable Brassica cultivars for planting. |
URL | http://www.plantwise.org/ |
Title | Xcc genomic sequences |
Description | Illumina genomic sequence from 4 Xcc race 4 isolates from Africa, including Kenya, Tanzania, Zambia & Namibia, 2 additional race 4 isolates from the UK and Portugal and a race 5 isolate from Tanzania has been produced. To ensure that this data will be used and accessible to African researchers, it will be incorporated into a pangenomic database of X. campestris that is currently being developed with collaborators at University of Exeter (led by David Studholme). This database has been assembled from reference genomes of standard races of the major Xcc pathovars. Genome sequence of the Xcc isolates will be released via GenBank along with publication in a refereed journal. |
Type Of Material | Database/Collection of data |
Year Produced | 2013 |
Provided To Others? | Yes |
Impact | Genome sequence of the Xcc isolates will be released via GenBank along with publication in a refereed journal. |
Description | EH Malvern Show 2012 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Co-PI (Holub) was a presenter at the Three Countries Agricultural Show, Malvern (16 June 2012). Engaged with members of the public on diseases in plants. a follow-up presentation at a stake-holder workshop on horticultural food security at the Warwick Crop Centre |
Year(s) Of Engagement Activity | 2012 |
Description | EH workshop on Hort Food Security |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Discussion of environmental & supply-chain factors that threaten food security not known |
Year(s) Of Engagement Activity | 2012 |
Description | JV Fascination of Plants day Oxford |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Huge number of visitors and huge interest. The event has grown and become an annual event with worldwide participants. |
Year(s) Of Engagement Activity | 2012 |
URL | http://www.plantday.org/ |
Description | JV contribution to Channel 4 TV Food Unwrapped programme |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Segment on role of Xanthomonas bacteria in food processing shown on 'Food Unwrapped' episode 6 on Oct 22 2012 Raised public awareness of use of microbial products in food industry. |
Year(s) Of Engagement Activity | 2012 |
URL | http://www.youtube.com/watch?v=dqvc-3Iub1E&feature=context-shows&list=SL |
Description | P Hand University Open Days |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | lively Q&A about careers in Agriculture and research Increase in student applications to Harper Adams University |
Year(s) Of Engagement Activity | 2013,2014 |
Description | PH article in 'Leading In Research' |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Brochure widely distributed at public open days and to policymakers and industry stakeholders. Also published online. difficult to quantify. |
Year(s) Of Engagement Activity | 2013 |
URL | http://www.harper-adams.ac.uk/publications/research/ |
Description | PH contribution to BBSRC Bioscience behind secure harvests |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | BBSRC publication 'Bioscience behind Secure Harvests' produced and widely distributed. not known. |
Year(s) Of Engagement Activity | 2010 |