There is emerging evidence that the geographical footprint of stripe rust is expanding, opening up prospects for an increase in economic losses attributable to this disease worldwide. Drawing on newly compiled data, along with insights obtained from a survey initiated at the BGRI meeting in New Delhi in August 2013, this talk will report on efforts to model the global occurrence and persistence of stripe rust in a geo-spatially sensitive fashion. Using the available data in conjunction with these newly developed climate suitability maps, I will present probabilistic crop production losses associated with the disease and place an economic value on the prospective losses. Given changes in the geographical spread of this disease, and the associated uncertainties about its likely wheat yield and economic effects, various scenarios will be assessed to inform and thereby help shape the research investment decisions regarding crop breeding and other options for ameliorating these prospective losses over the longer term.
Advances in breeding for resistance to stem rust caused by Ug99 and Ethiopian Pgt races in durum wheat
BGRI 2014 Plenary Abstract Karim Ammar
Stem rust (SR) resistance is required for CIMMYT durum germplasm to keep relevance in Ethiopia, where Ug99 and other Pgt races are a major yield-limiting constraint, and in countries along the possible dissemination paths of these races. Resistance to Ug99 is widespread in most durum germplasm groups when tested in Kenya, but resistance is lost when exposed to Ethiopian races; hence selection at the Debre Zeit site in Ethiopia is essential for durum wheat. Due to difficulties with shuttling segregating populations between Mexico and Ethiopia, we have adopted a strategy involving the identification of resistant/moderately resistant lines at Debre- Zeit, and inter-crossing in Mexico followed by selection for resistance to leaf rust and agronomic type and finally screening for SR reaction in the resulting F6 lines at Debre-Zeit at the same time as they are tested for yield and quality in preliminary yield trials in Mexico. This has generated a significant increase in the proportion of resistant and moderately resistant genotypes within outgoing CIMMYT germplasm, from less than 3% at the onset of the initiative in 2008 to 16% in 2011, and 38% in 2013. SR-resistant germplasm was characterized by similar frequency distributions to other traits in the overall germplasm such as yield potential, drought tolerance and industrial quality parameters. Advances have also been realized using marker-assisted selection (MAS) to introgress Sr22 from bread wheat and to combine it with Sr25, producing advanced lines with 2-gene stacks with confirmed outstanding resistance and superior quality attributes. Since the two genes are closely linked but from different sources bringing them together required a very rare recombination event finally detected via MAS among thousands of plants. They are now essentially inherited together with a very low likelihood of generating recombinant individuals with either gene. The yield potential and stability of these lines are under evaluation in Ethiopia and the best lines are being used in a second round of breeding.
Understanding resistance gene mediated recognition of stem rust in wheat
BGRI 2014 Plenary Abstract Peter Dodds
CSIRO Plant Industry, Australia
Stem rust caused by Puccinia graminis tritici (Pgt) is one of the most serious diseases in wheat and is combated mainly through the use of resistant varieties. Because the fungus evolves virulence towards previously resistant varieties, continuous breeding and identification of new sources of resistance are necessary to combat the threat of rust epidemics. Our work on the flax rust model system has provided insights into how the plant immune system recognises and responds to rust pathogens. We have been extending this work to wheat stem rust by targeted cloning of resistance (R) genes in wheat and corresponding Avr genes in Pgt. Plant R genes encode immune receptors that recognise and respond to pathogen effector proteins delivered into host cells from haustoria. We recently isolated the Sr33 and Sr50 resistance genes from wheat and have begun functional analyses to determine how they trigger defense responses. We are also targeting effectors from Pgt that are recognised by wheat R genes. We used genome and transcriptome sequencing to predict ~400 candidate effector genes from Australian Pgt race 21- 0. To screen for recognition of these proteins by wheat R genes, we developed a bacterial Type III Secretion System delivery assay using Pseudomonas fluorescens to inject the effector candidates into wheat leaf cells. We are screening candidate effectors on a set of 18 wheat cultivars carrying 22 different R genes and have so far identified one effector that induces a cell death response specifically on a wheat genotype carrying Sr22. Understanding the nature of wheat R genes and the Avr proteins that they recognize will allow better prediction of R gene durability and enable the possibility of rational design of novel R genes. We are also developing techniques for stacking R genes in cassettes for deployment of multiple genes at a single locus in wheat.
The discovery of Ug99 stem rust with virulence on most widely grown wheat cultivars worldwide triggered substantial new research on host resistance genes and associated virulence dynamics in the pathogen. Ug99 is mutating and migrating, with eight variants presently known, and has spread throughout eastern Africa, across the Red Sea to Yemen and Iran, and to South Africa. It has been speculated that further movement of Ug99 spores from South Africa to South America could happen on prevailing winds that occur about eight days per month on average. While Ug99 is not yet present in South America, this is a critical entry point into the Western Hemisphere as demonstrated by introduction of soybean rust to Paraguay in 2001. Thus, work was initiated to engage countries in South America to participate in monitoring for its occurrence. Stem rust surveys are currently conducted in Argentina, Brazil, and Uruguay on a regular basis. Each country has a national agricultural institute with adequate to good capacity to perform pathotyping work, but have limitations due to inadequate greenhouse cooling. We will present the current virulence dynamics of Pgt in each country. In addition to surveys for rust, we searched for the presence of Berberis spp. in Brazil. Berberis laurina was abundantly distributed in the Rio Grande du Sul state near the city of Caçapava. Leaves sampled in October displayed low to moderate aecial infections. Determination of the pathogen species infecting B. laurina is currently being determined by physiologic and molecular methods.
The shortage of stem rust resistance genes effective against the Ug99 group prompted recent efforts to increase the number of resistance genes available to breeders. We are fortunate that many new and/or cytogenetically improved rust resistance genes are now being shared with the global wheat breeding community by their developers. If we are poor stewards of these resources, the new resistance genes will eventually be defeated, and we will waste the efforts and investments that have been made. However, if we are good stewards, we should have enough resistance to achieve sustainable, durable resistance. Stewardship can be defined as the careful and responsible management of something entrusted to one’s care. What should we do to safeguard the new resistance genes? Diversification of resistance is often suggested as a way to reduce the risk of large scale epidemics. Although diversification is generally a good idea, it cannot be at the expense of leaving new genes exposed and vulnerable. A durable combination (pyramid) must be designed so that the component genes protect each other. They should reduce the probability of simultaneous pathogen mutations to virulence and they should avoid stepwise erosion of the pyramid by preventing significant reproduction of any new race that is virulent on component genes. We need pyramids to be immune or nearly immune not only to current races, but to anticipated mutants. This objective should be achievable with three or more major genes or a combination of major and minor genes. Successful gene stewardship will depend on several things. On the technical side, we will need very good markers for each gene. Each breeding program will require strong genotyping support to assemble and then validate pyramids. Most importantly, successful stewardship will require that we organize our user community to cooperate more closely. We will need to decide which genes require special stewardship and which do not. Every user of the stewardship pool resource will need to participate in earnest. It only takes one cultivar with an unprotected gene to give the pathogen a stepping stone to greater virulence. As they say, a chain is only as strong as the weakest link
Survey of barberry and associated rust pathogens in Nepal
BGRI 2013 Poster Abstract Maria Newcomb
USDA-ARS Arid Land Agricultural Research Center
Wheat contributes directly to food security and the national economy in Nepal. Of the rusts of wheat, stripe rust causes the most frequent and severe yield losses. Race changes can lead to damaging epidemics. To better understand factors that influence regional diversity of the stripe rust and stem rust pathogens, we surveyed rusts on barberry in 2012 and 2013. Nepal has a high diversity of barberry (30 species) and elevational habitats that extend the seasonal distributions of wheat and barberry. The greatest diversity occurs from 2,700 m and above, and distributions range from 1,200 to 4,500 m. We surveyed locations in all regions (central, eastern, western, and far-western) of the hill zone. Barberry was common between 1,300 and 1,800 m where wheat is grown. In the far-western region, barberry was found near all the wheat fields we surveyed. Between 1,300 and 1,800 m, Berberis asiatica is the most common species. B. aristata is present at the upper end of this range. Aecial infections on barberry occurred in patchy distributions in both 2012 and 2013. Collections of aecia on barberry were made at 5 locations and are being identified by inoculation studies using a range of grass hosts. Additionally, the rust samples are being evaluated by real-time PCR assays using species-specific ITS primer/probes for detection of Puccinia graminis or P. striiformis. Preliminary results for 32 single-aecia samples from 2012 were negative for P. graminis; 7 were positive for the P. striiformis complex.
Stocking the Breeder’s Toolbox: An update on the status of resistance to stem rust in wheat
BGRI 2012 Plenary Abstract Mike Pumphrey
Department of Crop and Soil Sciences, Washington State University, USA
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The number of designated stem rust resistance genes has increased by ~10 over the past four years. Translocations involving several broadly-effective alien resistance genes with limited or no previous agricultural deployment were enginneered to reduce the likelihood of linkage drag, and the foundations of adult plant resistance were established. This progress resulted from international collaboration, increased global coordination, and critical financial support. By buidling on these initial accomplishments and improving genetic and genomic resources over the next four years we expect to achieve: 1. more than 10 additional formally designated stem rust resistance genes conferring resistance to Ug99-complex races, 2. robust/diagnostic DNA marker haplotypes identified for most sources of resistance, 3. multiple linkage blocks of two or more resistance genes to enhance gene pyramiding efforts, and 4. knowledge of numerous additional sources of resistance complelely or partially identified. Never before have so many resources and supporting tools been available to combat the wheat rusts. It is an opportune time for the international community to strategically deploy and responsibly steward our genetic resources for durable control of wheat stem rust.
Stripe rust of wheat (yellow rust) is a recurring production constraint in the majority of wheat growing areas of the world. The transboundary nature of the pathogen coupled with its current virulence capabilities, favorable environmental conditions, sometimes overlapping and/or continuous cultivation of susceptible varieties in stripe rust-prone zones, and genetic uniformity of certain recent ‘mega-cultivars’ were major driving forces in stripe rust epidemics worldwide. Breeding for resistance must continue be the central pillar of stripe rust control, and for this to be effective there must be adequate pathogen monitoring combined with commitment to identify and incorporate diverse sources of resistance, preferably of the durable type. Deployment of resistance will only be successful if it is combined with high yield and appropriate end-use quality to meet the needs of farmers and consumers. Suitable seed systems need to be in place for timely distribution of varieties. This paper deals with the historical impacts and current status of stripe rust epidemics and highlights the need for regional and global collaboration in mitigating the global impact of this disease.
Success in seed multiplication and delivery efforts at UAS, Dharwad
BGRI 2012 Plenary Abstract R.R. Hanchinal
University of Agricultural Services, India
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Seed is a basic, vital and central input in agriculture and in all farming systems. Timely availability of quality seeds of varieties/hybrids adapted to to different agro-climatic conditions and in sufficient quantity at affordable prices is a measure of the strength and health of an agricultural economy. Sustained increase in agricultural production requires a continuous development of improved crop varieties/hybrids, an efficient system of production, and a means of distribution to farmers. India is one of the few countries where the seed sector has advanced in parallel with the agricultural production. However, the availability of quality seed of improved varieties and hybrids is grossly inadequate and is a major constraint to enhanced production. Studies made by several workers (Gadwal 2003, Patil et al 2004, Hanchinal et al. 2007) clearly indicate that with high-volume low-value seeds, such as wheat, groundnut, soybean and chickpea, 80% of the cropping area is sown with farm-saved seeds of old and obsolete varieties During last few decades, a number of high yielding disease and pest resistant varieties/hybrids in different crops had 10 to 40% yield superiority over local cultivars. With the exception of high-value low-volume seeds, seed production of low-value high-volume crops is generally left to public sector agencies. The bulky nature of most self pollinated crops, and lack of adequate investment on infrastructure means low remuneration. Although there is enough breeder seed production in most of the high volume crops, further seed multiplication through the foundation and certified seed stages are major constraints to the availability of quality seed. The present rate of seed replacement (SRR) for such crops is 6 to 8%. There is a need to increase SRR to 25 to 30% in varieties and obviously 100% for hybrids. To increase the productivity of low-value high-volume crops farmers need to have access to improved seeds of the right type, at the right time, at the right place and at a reasonable price. For supply of such seeds, both the informal seed sector (farmer managed seed systems) and the formal seed system (seed enterprises) need to be engaged. The informal seed sector is often highly effective in reaching isolated, inaccessible, small holder areas and is a sound opportunity for entrepreneurs to gradually evolve into the formal enterprises Wheat, the most important food crop of world and backbone of global food security, belongs to the highvolume low-value seed group. Of the total area sown to both hexaploid bread wheat and tetraploid durum and emmer wheat worldwide, 44% (95 m ha) is in Asia. Of this,62 m ha are located in just three countries viz. China, India, and Pakistan (Table 1 and Figure 1). Food security and production stability are of paramount importance in most Asian countries, given that the majority of farmers are poor. The wheat rusts have historically been major biotic constraints both in Asia and the rest of the world. Stem rust has been under control since the beginning of the green revolution in South and West Asia in the 1960s. Leaf rust and stripe rust continue to be major threats to production over approximately 60 (63%) and 43 (46%) m ha, respectively, in Asia. Although, the timely application of fungicides can provide adequate control, their use adds to production costs and they are considered environmentally unsafe. Growing resistant cultivars is thus the most effective and efficient control strategy, as it has no cost to farmers and is environmentally safe. Rapid evolution of races with new virulences, or combinations of virulences, dictate a need for discovery and deployment of new resistance genes and/or resistance gene combinations.
How has Lr34/Yr18 conferred effective rust resistance in wheat for so long?
BGRI 2012 Plenary Abstract Beat Keller
Institute of Plant Biology, University of Zurich, Switzerland
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The Lr34/Yr18 gene has been used in agriculture for more than 100 years. In contrast to many other resistance sources against leaf rust and stripe rust, it has remained effective and no virulence has been reported. This makes Lr34 a unique and highly valuable resource for rust resistance breeding. The pleiotropic nature of the gene conferring partial resistance to different pathogen species, the associated leaf tip necrosis and its durability suggest a molecular mechanism that is different from major gene resistance. This is supported by the molecular nature of Lr34 which was recently found to encode an ABC transporter. Interestingly, all tested wheat lines contain an allele of the Lr34 gene on chromosome 7DS. In its susceptible form, the gene does not confer resistance. The difference between the encoded resistant and susceptible LR34 isoforms consists of only two amino acid changes, whereas the rest of the proteins are identical. These two changes must change the biochemical properties of the resistant LR34 transporter in such a way that the plant becomes resistant. We speculate that there is a slight conformational change in the resistant form of the protein, resulting either in modified specificity or kinetics of the transported molecule, or that the binding properties to an unknown second protein interacting with LR34 are changed, resulting in altered function. While the molecular nature of the molecule(s) transported by the LR34 protein remains unclear, it is likely that a physiological change related to Lr34 activity is at the basis of resistance. We are currently establishing transgenic approaches in heterologous grass species to further investigate the molecular activity of Lr34 and to better understand a physiological mechanisms resulting in disease resistance.