Durable Disease Resistance Research Articles

Effective strategy for pyramiding three bacterial blight resistance genes into fine grain rice cultivar, Samba Mahsuri, using sequence tagged site markers

Bacterial leaf blight (BB) of rice is a major disease limiting rice production in several rice growing regions of the world. The pathogen, Xanthomonas oryzae pv oryzae, causing the disease is highly virulent to rice crops and is capable of evolving new races. Breeding efforts to incorporate single BB resistant gene often leads to resistance breakdown within a short period. To overcome such breakdown of resistance and develop germplasm with durable disease resistance, we have introgressed three bacterial blight resistance genes, xa5, xa13, and Xa21 into a fine grain rice variety, Samba Mahsuri, using sequence tagged site (STS) markers linked to these genes. Since the efficiency of the STS markers linked to recessive genes to detect homozygotes is less than 100%, we adopted four different pyramiding schemes to minimize loss of recessive resistance genes in advanced backcross generations. Pyramiding scheme A in which a two-gene Samba Mahsuri pyramid line containing Xa21 and xa5 genes was crossed with the Samba Mahsuri line having xa13 gene alone was found to be most effective in preventing the loss of an important recessive gene xa13. We further demonstrated that there was no yield penalty due to pyramiding of multiple genes into the elite indica rice variety.

A single plant resistance gene promoter engineered to recognize multiple TAL effectors from disparate pathogens

Plant pathogenic bacteria of the genus Xanthomonas inject transcription-activator like (TAL) effector proteins that manipulate the hosts' transcriptome to promote disease. However, in some cases plants take advantage of this mechanism to trigger defense responses. For example, transcription of the pepper Bs3 and rice Xa27 resistance (R) genes are specifically activated by the respective TAL effectors AvrBs3 from Xanthomonas campestris pv. vesicatoria (Xcv), and AvrXa27 from X. oryzae pv. oryzae (Xoo). Recognition of AvrBs3 was shown to be mediated by interaction with the corresponding UPT (UPregulated by TAL effectors) box UPT(AvrBs3) present in the promoter R gene Bs3 from the dicot pepper. In contrast, it was not known how the Xoo TAL effector AvrXa27 transcriptionally activates the matching R gene Xa27 from the monocot rice. Here we identified a 16-bp UPT(AvrXa27) box present in the rice Xa27 promoter that when transferred into the Bs3 promoter confers AvrXa27-dependent inducibility. We demonstrate that polymorphisms between the UPT(AvrXa27) box of the AvrXa27-inducible Xa27 promoter and the corresponding region of the noninducible xa27 promoter account for their distinct inducibility and affinity, with respect to AvrXa27. Moreover, we demonstrate that three functionally distinct UPT boxes targeted by separate TAL effectors retain their function and specificity when combined into one promoter. Given that many economically important xanthomonads deliver multiple TAL effectors, the engineering of R genes capable of recognizing multiple TAL effectors provides a potential approach for engineering broad spectrum and durable disease resistance.

How can we achieve durable disease resistance in agricultural ecosystems?

How can we achieve durable disease resistance in agricultural ecosystems?

Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice

Blast disease is a devastating fungal disease of rice, one of the world's staple foods. Race-specific resistance to blast disease has usually not been durable. Here, we report the cloning of a previously unknown type of gene that confers non-race-specific resistance and its successful use in breeding. Pi21 encodes a proline-rich protein that includes a putative heavy metal-binding domain and putative protein-protein interaction motifs. Wild-type Pi21 appears to slow the plant's defense responses, which may support optimization of defense mechanisms. Deletions in its proline-rich motif inhibit this slowing. Pi21 is separable from a closely linked gene conferring poor flavor. The resistant pi21 allele, which is found in some strains of japonica rice, could improve blast resistance of rice worldwide.

Marker-assisted Breeding for Disease Resistance in Potato

Sub-project 5 of BIOEXPLOIT aims to design durable disease resistance through marker-assisted breeding by converting existing markers for high-throughput application, developing and validating high-throughput marker technologies and pyramiding major R genes and/or quantitative trait loci into elite material. Activities include (1) the fine mapping of the quantitative trait locus PiXspg which accounts for a large proportion of the variation in late blight resistance, (2) converting SNP-based markers and an AFLP marker to easy-to-use-markers, (3) testing of progenies with combined sources of late blight resistance for presence of R genes and agronomic features, (4) backcrossing new sources of resistance to S. tuberosum and molecular screening of breeding materials with marker GP94 linked with gene Rpi-phu1 conferring late blight resistance, (5) evaluating potato clones with enhanced resistance against Phytophthora infestans under field conditions of Toluca (Mexico), and (6) developing populations and marker-assisted breeding for disease resistance.

The BIOEXPLOIT Project

The EU Framework 6 Integrated Project BIOEXPLOIT concerns the exploitation of natural plant biodiversity for the pesticide-free production of food. It focuses on the pathogens Phytophthora infestans, Septoria tritici, Blumeria graminis, Puccinia spp. and Fusarium spp. and on the crops wheat, barley, tomato and potato. The project commenced in October 2005, comprises 45 laboratories in 12 countries, and is carried out by partners from research institutes, universities, private companies and small-medium enterprises. The project has four strategic objectives covered in eight sub-projects. These objectives relate to (i) understanding the molecular components involved in durable disease resistance, (ii) exploring and exploiting the natural biodiversity in disease resistance, (iii) accelerating the introduction of marker-assisted breeding and genetic engineering in the EU plant breeding industry, and (iv) coordinating and integrating resistance breeding research, providing training in new technologies, disseminating the results, and transferring knowledge and technologies to the industry.

Next-Generation Communication

In the past decade, there have been major advances in our understanding of the molecular interplay between plants and various classes of microbial pathogens (bacteria, fungi, oomycetes, viruses, and nematodes) and microbial symbionts (rhizobia or mycorrhizal fungi). These fundamental insights, reviewed in a special section in this issue (p. 741), provide a conceptual framework for rational human intervention through the breeding or engineering of crops for durable and broad-spectrum disease resistance. However, such engineered plants will eventually be deployed into soils of varying geochemistry that harbor a staggering diversity of microbes. Many of these microbes can associate intimately with crops or other plants in natural habitats. A deeper understanding of plant-associated microbial communities is likely to offer exciting opportunities for controlling plant growth and pathogen burden in sustainable agricultural settings over the next two decades.

A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat

Agricultural crops benefit from resistance to pathogens that endures over years and generations of both pest and crop. Durable disease resistance, which may be partial or complete, can be controlled by several genes. Some of the most devastating fungal pathogens in wheat are leaf rust, stripe rust, and powdery mildew. The wheat gene Lr34 has supported resistance to these pathogens for more than 50 years. Lr34 is now shared by wheat cultivars around the world. Here, we show that the LR34 protein resembles adenosine triphosphate-binding cassette transporters of the pleiotropic drug resistance subfamily. Alleles of Lr34 conferring resistance or susceptibility differ by three genetic polymorphisms. The Lr34 gene, which functions in the adult plant, stimulates senescence-like processes in the flag leaf tips and edges.

Isolation and Manipulation of Quantitative Trait Loci for Disease Resistance in Rice Using a Candidate Gene Approach

Bacterial blight caused by Xanthomonas oryzae pv. oryzae and fungal blast caused by Magnaporthe grisea result in heavy production losses in rice, a main staple food for approximately 50% of the world's population. Application of host resistance to these pathogens is the most economical and environment-friendly approach to solve this problem. Quantitative trait loci (QTLs) controlling quantitative resistance are valuable sources for broad-spectrum and durable disease resistance. Although large numbers of QTLs for bacterial blight and blast resistance have been identified, these sources have not been used effectively in rice improvement because of the complex genetic control of quantitative resistance and because the genes underlying resistance QTLs are unknown. To isolate disease resistance QTLs, we established a candidate gene strategy that integrates linkage map, expression profile, and functional complementation analyses. This strategy has proven to be applicable for identifying the genes underlying minor resistance QTLs in rice-Xoo and rice-M. grisea systems and it may also help to shed light on disease resistance QTLs of other cereals. Our results also suggest that a single minor QTL can be used in rice improvement by modulating the expression of the gene underlying the QTL. Pyramiding two or three minor QTL genes, whose expression can be managed and that function in different defense signal transduction pathways, may allow the breeding of rice cultivars that are highly resistant to bacterial blight and blast.

Signaling in Plant Disease Resistance and Symbiosis

Interactions between plants and microbes result in plant disease and symbiosis. The former causes considerable economic damage in modern agriculture, while the latter has produced great beneficial effects to our agriculture system. Comparison of the two interactions has revealed that a common panel of signaling pathways might participate in the establishment of the equilibrium between plant and microbes or its break-up. Plants appear to detect both pathogenic and symbiotic microbes by a similar set of genes. All symbiotic microbes seem to produce effectors to overcome plant basal defenses and it is speculated that symbiotic effectors have functions similar to pathogenic ones. Signaling molecules, salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), are involved in both plant defense and symbiosis. Switching off signals contributing to deterioration of disease symptom would establish a new equilibrium between plant and pathogenic microbes. This would facilitate the development of strategies for durable disease resistance.

Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance

To manipulate host defences, plant pathogenic oomycetes secrete and translocate RXLR effectors into plant cells. Recent reports have indicated that RXLR effectors are translocated from the extrahaustorial matrix during the biotrophic phase of infection and that they are able to suppress PAMP-triggered immunity. Oomycete genomes contain potentially hundreds of highly diverse RXLR effector genes, providing the potential for considerable functional redundancy and the consequent ability to readily shed effectors that are recognised by plant surveillance systems without compromising pathogenic fitness. Understanding how these effectors are translocated, their precise roles in virulence, and the extent to which functional redundancy exists in oomycete RXLR effector complements, are major challenges for the coming years.

Discovery and genetic mapping of single nucleotide polymorphisms in candidate genes for pathogen defence response in perennial ryegrass (Lolium perenne L.)

Susceptibility to foliar pathogens commonly causes significant reductions in productivity of the important temperate forage perennial ryegrass. Breeding for durable disease resistance involves not only the deployment of major genes but also the additive effects of minor genes. An approach based on in vitro single nucleotide polymorphism (SNP) discovery in candidate defence response (DR) genes has been used to develop potential diagnostic genetic markers. SNPs were predicted, validated and mapped for representatives of the pathogenesis-related (PR) protein-encoding and reactive oxygen species (ROS)-generating gene classes. The F(1)(NA(6) x AU(6)) two-way pseudo-test cross population was used for SNP genetic mapping and detection of quantitative trait loci (QTLs) in response to a crown rust field infection. Novel resistance QTLs were coincident with mapped DR gene SNPs. QTLs on LG3 and LG7 also coincided with both herbage quality QTLs and candidate genes for lignin biosynthesis. Multiple DR gene SNP loci additionally co-located with QTLs for grey leaf spot, bacterial wilt and crown rust resistance from other published studies. Further functional validation of DR gene SNP loci using methods such as fine-mapping and association genetics will improve the efficiency of parental selection based on superior allele content.

Durable resistance to wheat stem rust needed

The recent outbreak of a new wheat stem rust race capable of parasitizing many commercial wheat cultivars highlights the need for durable disease resistance in crop plants. More advanced breeding approaches using quantitative disease resistance genes and resistance gene pyramids are being used to combat wheat stem rust and other diseases, though widespread adoption of these breeding methodologies is needed to maintain resistance efficacy. Advances in understanding the molecular basis of plant disease resistance at both host and nonhost levels offers further possibilities for stem rust resistance using biotechnological approaches. However, truly durable resistance to wheat stem rust and other phytopathogens seems an unlikely prospect in the face of continually evolving pathogen populations.

An anchored linkage map for sugar beet based on AFLP, SNP and RAPD markers and QTL mapping of a new source of resistance to Beet necrotic yellow vein virus

Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), is an important sugar-beet disease worldwide and can result in severe losses of root yield and sugar content. We have identified a major QTL for BNYVV resistance from a new source in a segregating population of 158 individuals. The QTL explained an estimated 78% of the observed phenotypic variation and the gene conferring the partial resistance is referred to as Rz4. AFLP was used in combination with bulked segregant analysis (BSA) to develop markers linked to the resistance phenotype. AFLP marker analysis was extended to produce a linkage map that was resolved into nine linkage groups. These were anchored to the nine sugar-beet chromosomes using previously published SNP markers. This represents the first anchored sugar-beet linkage map to be published with non-anonymous markers. The final linkage map comprised 233 markers covering 497.2 cM, with an average interval between markers of 2.1 cM. The Rz4 QTL and an Rz1 RAPD marker were mapped to chromosome III, the known location of the previously identified BNYVV resistance genes Rz1, Rz2 and Rz3. The availability to breeders of new resistance sources such as Rz4 increases the potential for breeding durable disease resistance.

More precise map position and origin of a durable non-specific adult plant disease resistance against stripe rust (Puccinia striiformis) in wheat

Recently a major gene determining non-specific adult plant disease resistance against stripe rust (Puccinia striiformis) designated Yrns-B1 was mapped in wheat Triticum aestivum L. by using a cross between ‘Lgst. 79-74’ (resistant) and ‘Winzi’ (susceptible). Linkage to five Gatersleben wheat microsatellite (GWM) markers was discovered, previously mapped on chromosome arm 3BS. In the present study this map was improved by the incorporation of four additional GWM markers. QTL-analysis revealed high LOD values for the resistance at all nine loci, whereas the largest LOD (20.76) was found for the newly mapped marker Xgwm1329.

Farmers’ participation and breeding for durable disease resistance in the Andean region

In the Andean region, the Preduza project and its partners combined breeding for durable disease resistance using locally adapted cultivars and farmer participatory methods. The approach taken resembles participatory variety selection (PVS). Farmers participated in the selection of advanced materials, rather than finished cultivars. This paper describes this approach and reports experiences with farmers–breeders collaboration.

Introduction: focusing on breeding for durable disease resistance of the Andean highland food crops

The Andes forms a long chain of mountains of over 7,000 km long that range form Southern Venezuela to the South of Chile. The crops discussed in this issue are grown at altitudes ranging from 1,500 m to over 4,000 m in a very heterogeneous environment, characterised by large differences in rainfall, humidity and temperature. Also the latitude and direction of the slopes have significant effects on the amount and distribution of rainfall. Farmers have great experiences and skills in adapting their farming systems to these specific conditions. In the Andean region the majority of the farmers can be classified as low input small-holders, typical for marginal areas.

Applying innovations and new technologies for international collaborative wheat improvement

Despite the successes of the Green Revolution, about a billion people are still undernourished and food security in the developing world faces new challenges in terms of population growth, reduced water resources, climate change and decreased public sector investment. It is also becoming widely recognized that poverty is a cause of environmental degradation, conflict and civil unrest. Internationally coordinated agricultural research can play a significant role in improving food security by deploying promising new technologies as well as adapting those with well-established impact.In addition to the genetic challenges of crop improvement, agriculturalists must also embrace the problems associated with a highly heterogeneous and unpredictable environment. Not only are new genetic tools becoming more accessible, but a new generation of quantitative tools are available to enable better definition of agro-ecosystems, of cultivar by environment interactions, and of socio-economic issues, while satellite imagery can help predict crop yields on large scales. Identifying areas of low genetic diversity – for example as found in large tracts of South Asia – is an important aspect of reducing vulnerability to disease epidemics. Global strategies for incorporating durable disease resistance genes into a wider genetic background, as well as participatory approaches that deliver a fuller range of options to farmers, are being implemented to increase cultivar diversity.The unpredictable effects of environment on productivity can be buffered somewhat by crop management practices that maintain healthy soils, while reversing the consequences of rapid agricultural intensification on soil degradation. Conservation agriculture is an alternative strategy that is especially pertinent for resource-poor farmers.The potential synergy between genetic improvement and innovative crop management practices has been referred to as the Doubly Green Revolution. The unique benefits and efficiency of the international collaborative platform are indisputable when considering the duplications that otherwise would have been required to achieve the same impacts through unilateral or even bilateral programmes. Furthermore, while the West takes for granted public support for crucial economic and social issues, this is not the case in a number of less-developed countries where the activities of International Agricultural Research Centres (IARCs) and other development assistance organizations can provide continuity in agricultural research and infrastructure.

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

BackgroundRice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.ResultsWe have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes.ConclusionBecause the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested.

Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat

The incorporation of effective and durable disease resistance is an important breeding objective for wheat improvement. The leaf rust resistance gene Lr34 and stripe rust resistance gene Yr18 are effective at the adult plant stage and have provided moderate levels of durable resistance to leaf rust caused by Puccinia triticina Eriks. and to stripe rust caused by Puccinia striiformis Westend. f. sp. tritici. These genes have not been separated by recombination and map to chromosome 7DS in wheat. In a population of 110 F(7) lines derived from a Thatcher x Thatcher isogenic line with Lr34/Yr18, field resistance to leaf rust conferred by Lr34 and to stripe rust resistance conferred by Yr18 cosegregated with adult plant resistance to powdery mildew caused by Blumeria graminis (DC) EO Speer f. sp. tritici. Lr34 and Yr18 were previously shown to be associated with enhanced stem rust resistance and tolerance to barley yellow dwarf virus infection. This chromosomal region in wheat has now been linked with resistance to five different pathogens. The Lr34/Yr18 phenotypes and associated powdery mildew resistance were mapped to a single locus flanked by microsatellite loci Xgwm1220 and Xgwm295 on chromosome 7DS.