Implementing effective marker technologies into disease resistance wheat breeding programmes within Africa

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

In a world economy faced with global food insecurity the demand for increased agricultural production has never been greater. This demand is set against a background of declining natural resources, increasing land marginalisation and the uncertainties of climate change. The development of low-chemical input, sustainable agricultural systems is therefore critical. Along with rice and maize, wheat provides a substantial proportion of the calorific intake of the human population. Biotic stresses present a major constraint to crop production, with the fungal rusts of wheat being a significant, global problem.
While the devastation caused by disease is an issue for all wheat growing regions of the world the problem is confounded in those countries where low wheat yields and the general economic climate prohibit the use of fungicides. This is never more apparent than for resource poor, small scale farmers in Africa.
In 1999 a new race of stem rust appeared in Uganda, overcoming the resistance present in 70% of wheat varieties. This new race, commonly known as Ug99 contributed to the global wheat price increases seen in 2007 and 2008, with the price of a loaf of bread in east Africa increasing by 70%. In 2000 a new, more aggressive race of stripe rust was detected in the US which was able to grow at higher temperatures. This race was found in Europe in 2001 and Western Australia in 2002, where previously the warmer climate was not conducive to stripe rust infection. This represented the fastest reported spread of a new pathogen race. It is therefore vital that sustainable wheat production systems are put in place. The development of high-yielding, disease resistant wheat varieties will go a long way to achieve this.
In this project we undertake a genetic and biological characterisation of a number of sources of novel resistance to stem and stripe rust, which has proven effective against these two diseases in southern and eastern Africa. The genes responsible for the resistance will be genetically defined using DNA markers to locate the position of the genes and measure the contribution of each to the overall resistance. Biological studies will inform as to the mechanisms of resistance such gene confers, thereby informing wheat breeders which genes to accumulate into new wheat varieties to obtain additive effects.
DNA markers will be developed for each resistance gene using the latest marker technologies. DNA markers provide tools by which wheat breeders can pyramid a number of resistance genes, allow for the development of superior wheat varieties in a much reduced time frame.
To ensure that these DNA markers can be used by national wheat breeding programmes within Africa two marker platforms will be established within research and breeding institutes in South Africa and Kenya. The project therefore contains a large capacity building programme, providing physical infrastructure and trained personnel. A knowledge-technology transfer pipeline will be established from the UK into Africa, using RSA and Kenya as the entry points, which will function both during the lifetime of this grant and beyond.

Technical Summary

The project has four major objectives:
Objective (1) will genetically locate and characterise sources of adult plant resistance (APR) to the fungal disease stem rust, causal agent Puccinia graminis f. sp. tritici in wheat. Four wheat mapping populations are available which segregate for field resistance to stem rust races prevalent in eastern Africa and commonly known to the Ug99 lineage. Genetic maps will be constructed for each population using SSR, DArT and SNP markers, followed by QTL analyses. The SNP markers will be designed to represent over 1000 wheat genes identified as responding to fungal infection as part of a global transcriptomics analysis in an ERA-PG project. KBioscience KASPar marker technology will be used to develop markers to SNPs identified within the resistance-related genes.
Objective (2) will use advanced microscopy to determine the cellular changes that occur within wheat flag leaves as a consequence of the presence of a stripe rust APR gene, and at what stage in fungal development the resistance gene effectively halts fungal invasion. This will provide a description of the possible mechanism of resistance conferred by each APR genes and the consequence on combining two or more such genes, with different mechanisms, on the overall level of rust resistance.
To enable Africa national wheat breeding programmes to incorporate the rust resistance genes identified into new wheat varieties for African farmers Marker Assisted Selection DNA marker platforms will be established in partner labs in South Africa and Kenya, Objective (3) . This project therefore has a large capacity building component, providing both physical infrastructure, training of skilled personnel (Objective 4), and the next generation of senior wheat researchers (Project student). A knowledge-technology transfer pipeline will be established from the UK into Africa, using RSA and Kenya as the entry points, which will function both during the lifetime of this grant and beyond.

Planned Impact

This project will lead to the production of new, superior wheat varieties with durable resistance to the devastating diseases of stem and stripe rust. These wheat varieties will support a sustainable wheat production system in Africa, being of considerable value to both small and large scale farmers. For small holder farmers in Africa wheat is a cash crop, providing money for things like schooling. Over 70% of small scale farmers in Kenya grow wheat, but only contribute 30% to the annual wheat harvest. Small scale farmers on average obtain wheat yields of 2 tonnes per ha compared to the 4 tonnes per ha of large scale farmers in Kenya. For these resource poor wheat farmers fungicides are not an option. Improved varieties will reduce the cost of production by more than 40% and increase yield per hectare by over 30%.
South Africa used to be an exporter of wheat. However, increased input cost, i.e. fungicides and loss of yields due to biotic and abiotic stresses, resulted in South Africa having to import wheat to meet human demand. Disease resistant, high yielding wheat varieties will therefore provide a resource that will benefit the big wheat farmer, and thus the general economy in Africa, but also small holder farmers, enhancing their livelihoods and helping to raise them out of poverty.
The establishment of advanced DNA marker platforms in South Africa and Kenya will allow wheat breeders to implement affordable Marker Assisted Selection strategies into their national breeding programmes. It will ensure diversity in the resistance genes deployed, the genetic basis of resistance breeding currently being somewhat narrow in South Africa, enabling wheat breeders to produce superior wheat varieties in half the time it currently takes to realise a new variety. The potential exists for realising seed of new wheat varieties in 5-6 years, ready for seed multiplication, rather than the current 10-13 years.
The role played by the partners in South Africa and Kenya in the wider wheat breeding industry in southern and eastern Africa, respectively, will also support the application of marker technologies in neighbouring countries. The materials developed will also be of value and application to the international wheat breeding programmes, including the spring wheat programmes of CIMMYT and ICARDA, and national programmes in the Middle East and Asia where again stem and stripe rust are serious disease problems.
The knowledge gained by the partners during this project, along with the training of the next generation of senior wheat researchers will ensure that academically Africa is not further marginalised from the global research community. The access to advanced DNA marker technologies, and the establishment of physical and human capacity will also enable the African partners to collaborate with the west in future research initiatives.
For the UK the new sources of stripe rust resistance will be included in the wheat pre-breeding programme at NIAB, and from there be passed to UK wheat breeders for further evaluation. This will provide well characterised and potentially new sources of stripe rust resistance for European wheat breeding. While stem rust is not a field disease in the UK, many parts of eastern and southern Europe are seeing an increase in stem rust. Therefore the new sources of stem rust resistance will also be of value to European wheat breeding.
 
Description Four Annual Reports and Three Case Studies have been submitted to BBSRC.
Exploitation Route The resources identified are already being used by wheat breeders in South Africa and Kenya.
Sectors Agriculture, Food and Drink

URL http://www.niab.com/pages/id/377/Dr_Lesley_Boyd
 
Description This four year project is now complete. The KASP marker platform is now used routinely in commercial wheat breeding programmes, provided as a Marker-Assisted Selection service by CenGen. The new sources of stem rust resistance and the corresponding markers have been integrated into these commercial wheat breeding programmes. The DNA markers developed for stripe and stem rust resistance sources have been incorporated in to the wheat breeding programs of 3 wheat breeding companies/public institutes within South Africa. In part the KASPar marker platform purchased by this project for the lab of renee Prins led to the South African Winter Cereal Trust providing funds to Dr Renee Prins, CenGen to provide a DNA marker service to the wheat breeding industry within South Africa for an initial period of 5 Years.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic,Policy & public services

 
Description New collaboration established with Diane Saunders, Earlham Institute, Norwich, UK 
Organisation The Genome Analysis Centre (TGAC)
Country United Kingdom 
Sector Public 
PI Contribution Joint supervision of a PhD student from South Africa
Collaborator Contribution Joint supervision of a PhD student from South Africa. Expanded research into a genome study of Puccinia striiformis population in South Africa.
Impact Conference oral and poster presentations
Start Year 2014
 
Description 11th SAPBA Symposium. March 8-10, 2016. Protea Hotel Technopark, Stellenbosch. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Van Schalkwyk, H.J., R. Prins, Z.A Pretorius, L.A. Boyd. C. Uauy and D.G.O. Saunders. 2016. Pathogenomics of South African stripe rust in a global context. 11th SAPBA Symposium. March 8-10, 2016. Protea Hotel Technopark, Stellenbosch.
Year(s) Of Engagement Activity 2016
 
Description 14th International Cereal Rusts and Powdery Mildews Conference, Helsingor, Denmark, 5-8th July 2015 (invited oral by 1st author). 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Castelyn, H.D., L.L. du Preez, B. Visser & Z. A. Pretorius. 2015. An integrated approach to understanding adult plant resistance: histology and molecular features of stem rust on wheat. 14th International Cereal Rusts and Powdery Mildews Conference, Helsingor, Denmark, 5-8th July 2015 (invited oral by 1st author).
Year(s) Of Engagement Activity 2015
 
Description 7th BGRI Technical Workshop, Sydney, Australia, 17-20th Sept. 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Van Schalkwyk, H.J., R. Prins, Z.A. Pretorius, L.A. Boyd, C. Uauy & D.G.O. Saunders. Placement of South African stripe rust in a global context and development of diagnostic tools for genotyping field samples. 7th BGRI Technical Workshop, Sydney, Australia, 17-20th Sept. 2015
Year(s) Of Engagement Activity 2015
 
Description International Congress for Molecular Plant Microbe Interactions, Portland, OR, USA. 17-21 th July, 2016 (invited oral presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Van Schalkwyk, HJ; Pretorius, ZA; Boyd, LA; Uauy, C; Prins, R; Saunders, DGO. (2016). Pathogenomics of South African stripe rust populations. International Congress for Molecular Plant Microbe Interactions, Portland, OR, USA. 17-21 th July, 2016 (invited oral presentation)
Year(s) Of Engagement Activity 2016
 
Description 11th SAPBA Symposium. March 8-10th 2016. Protea Hotel Technopark, Stellenbosch. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Prins, R., Susanne Dreisigacker, Zakkie Pretorius, Elsabet Wessels, Hester van Schalkwyk, Corneli Smit, Cornel Bender, Davinder Singh, Lesley Boyd. 2016. QTL validation of marker-trait associations in a diverse panel of African wheat. 11th SAPBA Symposium. March 8-10th 2016. Protea Hotel Technopark, Stellenbosch.
Year(s) Of Engagement Activity 2016
 
Description 11th SAPBA Symposium. March 8-10th 2016. Protea Hotel Technopark, Stellenbosch. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Visser B, Terefe TG, Herselman L and Pretorius ZA, 2016. Ten years of genotypic analysis of the three wheat rusts in southern Africa. 11th SAPBA Symposium. March 8-10th 2016. Protea Hotel Technopark, Stellenbosch.
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at a conference-Lesley Boyd 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The presentation resulted in further discussion with colleagues and peers.

None that were noticed
Year(s) Of Engagement Activity 2014
 
Description Presentation by Renee Prins II 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Participants in your research and patient groups
Results and Impact Presentation stimulated interest in technology.

Not aware of any
Year(s) Of Engagement Activity 2014
 
Description invited Keynote Speaker 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Pretorius, Z.A. 2016. Five critical concepts in breeding for rust resistance. 11th SAPBA Symposium. March 8-10, 2016. Protea Hotel Technopark, Stellenbosch
Year(s) Of Engagement Activity 2016