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.     

The return ofPhytophthora infestans, a potato pathogen that just won't quit

Summary Since the early 1980s and continuing through the end of the 20^th century, potato late blight caused byPhytophthora infestans has become noticeably more problematic throughout the world. Exotic strains of the pathogen are largely responsible for the increased problems. The new strains were initially detected in Europe, but subsequently they have been detected in Asia, the Middle East, South America and North America. Populations in the Middle East and South America may represent secondary migrations from Europe. Several independent migrations have occurred such that migrant populations in North America are very different from those in Europe. Also, population structures ofP. infestans are different in different worldwide locations. In some locations the migrant strains are resistant to metalaxyl, but in other locations either migrant or indigenous strains may be resistant. In most locations, the migrant strains are more aggressive than the previous indigenous strains.     

Review: Powdery Scab of Potato—Increased Knowledge of Pathogen Biology and Disease Epidemiology for Effective Disease Management

The importance of the potato tuber disease powdery scab, caused by the zoosporic pathogen Spongospora subterranea f. sp. subterranea, has increased worldwide, and the disease is one of the most important problems facing potato production in some regions. This soilborne pathogen produces many resting spores which can remain dormant for long periods, are highly resistant to environmental stresses and can spread the disease on seed potatoes and in contaminated soil. The enigmatic nature of this organism exacerbates the development of effective powdery scab control methods. Substantial knowledge has been gained in the last decade on the biology of the pathogen and the epidemiology of the disease, but no single effective control measure is, or is likely to be, available. An integrated approach to powdery scab management is the aim, with host resistance as a substantial and sustainable component. Further research on the epidemiology of powdery scab and population genetics of the pathogen is urgently required. All stakeholders involved in the potato industry must become aware that solution of the powdery scab problem is likely to be a long-term goal. When resistant cultivars with all the other characteristics demanded for marketing high-quality potatoes are available, and when disease risk from the pathogen on seed and/or in soil can be accurately determined, then the mission to develop effective powdery scab control will become achievable.     

Possible geographical origin ofPhoma exigua var.foveata,the principal causal organism of potato gangrene

Summary The highlands of South America are the probable geographic origin for the potato gangrene fungusPhoma exigua var.foveata (Foister) Boerema which was found parasitizing plants ofChenopodium quinoa in the Altiplano area of Peru. In vitro studies showed no dissimilarities between it and the antibiotic ‘E’ producing virulent European isolates ofP. exigua var.foveata. It is as pathogenic to potatoes as the virulent European isolates but onC. quinoa andC. album it is more pathogenic than the European isolates. So far the fungus has not been found on potato tubers in South America and the reasons why gangrene problems have not arisen there are discussed.     

Changes in the distribution of phenylamide-resistant strains ofPhytophthora infestans (Mont.) de Bary in Ireland 1985–89

Summary Phenylamide-based fungicides were reintroduced to the Irish market in 1985. Mixtures of phenylamides and mancozeb were recommended for no more than 3 sprays in potato late blight control programmes with the last systemic spray to be applied not later than 31 July. Samples of potato foliage infected withP. infestans were collected from the main potato growing areas in Ireland over a five-year period starting in 1985. Using the floating disc method, 11% of the crops sampled in 1985 were found to have phenylamide-resistant strains ofP. infestans present. The number of crops with resistant strains increased rapidly up to 1988 when 83% of the crops sampled had resistance. Factors affecting the distribution of resistance and the efficacy of a phenylamide-based spray programme are discussed.     

The current status of knowledge on the cellular biology of potato

Summary Conventional potato breeding does not make full use of the existing biodiversity within theSolanum genus. Moreover breeding at the 4x-4x level is slow. The potential for breeding at the diploid and dihaploid levels has therefore been explored. This requires use of novel techniques to overcome deviations from the desired Endosperm Balance Number. Somatic hybridization approaches include symmetric and asymmetric hybridizations and cybridization. Interesting traits have been successfully transferred through these techniques. Introgression and chromosome elimination have profited from the recent and rapid development of analytical techniques such as RFLP and RAPD. Cellular approaches in potato breeding may be combined with conventional breeding by a stepwise reduction of the ploidy level followed by resynthesis of a new heterozygous tetraploid clone. Such schemes have been used to include virus or nematode resistance. Haploids may be derived from different sources or obtained through different techniques. Dihaploid-dihaploid breeding programmes may be especially interesting. Because of this potential, cellular biology of potato deserves the continued interest of the scientific community.     

Limits to Growth or Growth to the Limits? Trends and Projections for Potatoes in China and Their Implications for Industry

While output for potatoes in China averaged nearly 73 million metric tonnes in 2008–2010, the trends for production, area, and yield have been far more volatile than suggested in earlier studies. A new set of estimated growth rates for potato production in China during the last five decades based on FAO times series data found that periods of rapid expansion were then followed by ones of stagnation and decline. Although increases in potato output have been impressive, China’s share of both regional and global production has declined in recent years as a result. This paper analyses these and other dimensions to the evolution of potato production in China during the last half century by synthesizing previous research before reassessing alternative future projections, highlighting opportunities for industry, and identifying some key topics for future research.     

Elucidation of the sex pheromone system of the potato tuberworm moth,Phthorimaea operculella (Zeller) (Lepidoptera,Gelechiidae): a short review

Summary Recent research, reviewed here, of the pheromone system of the potato tuberworm moth has led to the isolation, identification, and synthesis of its components.trans-4,cis-7-tridecadien-l-ol acetate (PTM 1) andtrans-4,cis-7,cis-10-tridecatrien-l-ol acetate (PTM 2), mixtures of which are much more attractive in the field than 2 virgin female moths or each compound on its own.     

Protease inhibitor activity is associated to a basic chitinase from potato but not to an acidic one

Summary Several pathogenesis-related proteins, which are produced in plants submitted to stress, have been identified as chitinases. We have previously described that a potato basic chitinase strongly inhibited the activity of an aspartic protease isolated from the same source. In this work, we have tested the activity of two potato chitinases as protease inhibitors. A basic chitinase (ChiB) inhibited trypsin, chymotrypsin, subtilisin, proteinase K and a serine protease ofFusarium sp. An acidic one (ChiA) did not show inhibitory activity. The kinetics of trypsin inhibition by ChiB revealed different patterns of inhibition with azocasein and BAPNA. Metal ions affected differentially both activities, suggesting that ChiB is a bifunctional protein. These results and those reported by other authors suggest a new physiological role for pathogenesis-related proteins. However, results presented in this paper suggest that the protease inhibitor activity is not a general characteristic of potato chitinases.     

Pathology and control of soil-borne fungal pathogens of potato

Summary Several soil-borne fungal pathogens continue to cause problems in potato production worldwide. The reasons for these problems are illustrated by reference to the pathogensVerticillium dahliae, Rhizoctonia solani, Spongospora subterranea and a group normally considered to be tuber-borne, includingColletotrichum coccodes, Helminthosporium solani andFusarium species. Generally, the long-term persistence of survival structures, the difficulties in reducing inoculum and lack of good sources of resistance hinder attempts to improve control of soil-borne fungal pathogens. Post-harvest fungicide treatment of seed or ware potatoes does not entirely alleviate storage problems. In the foreseeable future there is no alternative to the use of integrated measures from the time of planting seed to movement from storage. Key research areas that arise as a means of better controlling most of these pathogens are: the role of intraspecific variation in pathogenesis and ecology, problems of detecting and quantifying inoculum, and the need for improved methods for biological control.     

Cisgenesis Does Not Solve the Late Blight Problem of Organic Potato Production: Alternative Breeding Strategies

Average potato yields in Dutch organic farming systems vary from 15 to 29 Mg/ha and are limited by low input of nitrogen and severe late blight attacks caused by the oomycete Phytophthora infestans. Under Dutch late blight regulations it is mandatory to kill the haulm at 7% infestation. The late blight attacks have been so early in the organic potato production of the past few years that its acreage is now gradually decreasing whereas consumer demand is increasing. Agronomic control strategies have limited success. First priority lies in breeding for highly resistant varieties to safeguard organic potato production in the Netherlands. Cisgenesis, however, is not an option for the organic sector. Although the product of cisgenesis does not contain genes from non-crossable species it is a result of a genetic engineering process which is excluded from use in organic agriculture. As the principles and standards of organic agriculture are process-based, cisgenesis does not comply with the norms and standards of organic agriculture. The arguments of the organic sector go well beyond the alleged risks of the gene technology and relate to the technology itself. Breeding at DNA-level, instead of at whole-plant level, violates the integrity of life as described in the concept of naturalness. The Dutch organic sector is now aiming at increasing the traditional breeding activities including the participation of farmer-breeders in close cooperation with the formal breeding companies. Additional selection methods need to be developed to include required traits other than late blight resistance, such as nutrient efficiency. Recently two varieties have been released with high resistance against late blight based on introgressing genes from Solanum bulbocastanum. Organic agriculture can benefit from marker assisted breeding to achieve adequate pyramiding of different, new sources of resistance.     

Emerging and Re-emerging Potato Diseases in the Andes

Outbreaks of a new mating type (A2) of late blight (Phythopthora infestans) and the spread of bacterial wilt (Ralstonia solanacearum) were the most notable events among fungi and bacteria during the last 10 to 15 years in the Andes. The emergence of the A2 mating type of P. infestans was probably a result of seed movement from the Northern hemisphere. Black scurf caused by the fungus Rhizoctonia solani spread in Peru and Bolivia causing economic losses estimated at 5 to 10%. A high incidence of common scab on potato tubers, caused by the bacteria Streptomyces scabies was found in some localities in Bolivia. Among the emerging viruses, the NTN strains of PVY have been found in some countries including Peru. Recently, two other viruses have been found spreading in potatoes. One is coded SB26/29 and is transmitted by Russelliana solanicola, the first psyllid vector found for a plant virus. The other emerging virus is coded SB41 and is apparently also new to potatoes. It causes a severe mosaic on the affected plants and the virus is transmitted experimentally only by grafting. Some other viruses of minor importance have also been detected in potatoes.     

Cisgenesis,a New Tool for Traditional Plant Breeding,Should be Exempted from the Regulation on Genetically Modified Organisms in a Step by Step Approach

Modern potato breeding requires over 100,000 seedlings per new variety. Main reasons are (1) the increasing number of traits that have to be combined in this tetraploid vegetatively propagated crop, and (2) an increasing number of traits (e.g., resistance to biotic stress) originates from wild species. Pre-breeding by introgression or induced translocation is an expensive way of transferring single traits (such as R-genes, coding for resistance to biotic stress) to the cultivated plant. The most important obstacle is simultaneous transfer of undesired neighbouring alien alleles as linkage drag. Stacking several genes from different wild sources is increasing this linkage drag problem tremendously. Biotechnology has enabled transformation of alien genes into the plant. Initially, transgenes were originating mainly from microorganisms, viruses or non-crossable plant species, or they were chimeric. Moreover, selection markers coding for antibiotic resistance or herbicide resistance were needed. Transgenes are a new gene source for plant breeding and, therefore, additional regulations like the EU Directive 2001/18/EC were developed. Because of a strong opposition against genetic modification of plants in Europe, the application of this Directive is strict, very expensive, hampering the introduction of genetically modified (GM) crops and the use of this technology by small and medium-sized enterprises (SMEs). Currently, GM crops are almost the exclusive domain of multinationals. Meanwhile, not only transgenes but also natural genes from the plant species itself or from crossable plant species, called cisgenes, are available and the alien selection genes can be avoided in the end product. This opens the way for cisgenic crops without alien genes. The existing EU directive for GM organisms is not designed for this new development. The cisgenes belong to the existing breeders’ gene pool. The use of this classical gene pool has been regulated already in agreements regarding breeders’ rights. We are proposing a step by step approach starting with a crop and gene specific derogation and monitoring towards a general exemption of cisgenic plants from the Directive. Two examples, i.e. development of cisgenic potato for resistance to Phytophthora infestans and cisgenic apple for resistance to Venturia inaequalis are discussed shortly for illustration of the importance of cisgenesis as a new tool for traditional plant breeding. Cisgenesis is simplifying introgression and induced translocation breeding tremendously and is highly recommended for SMEs and developing countries.     

Benchmarking Food Crop Markets in Southern Africa: The Case of Potatoes and Potato Products 1961–2010

Pressures and opportunities in food systems across Southern Africa have generated renewed interest in potatoes both as a food crop and a source of income in recent years. With populations growing at over 2.0 %/year in several countries and urban consumers often eager to diversify their diets, new markets are also opening up. Given these trends, growers, traders and governments are seeking out new ways to capitalize on these developments. This paper examines the evolution of growth rates in potato production, utilization and trade in Southern Africa over nearly the last half century using FAO annual secondary data. After highlighting the different roles that potatoes have played in crop diversification across the sub-region, the paper identifies some key issues for future research as well as some opportunities for industry both large and small.     

Progress in Mapping and Cloning Qualitative and Quantitative Resistance Against <Emphasis Type="Italic">Phytophthora infestans</Emphasis> in Potato and Its Wild Relatives

Cultivated potato is susceptible to many pests and pathogens, none of which is more of a threat to potato agriculture than the late blight disease, caused by the oomycete Phytophthora infestans (Mont.) de Bary. To date all efforts to thwart this most adaptive of pathogens have failed, and early attempts to deploy ‘R genes’ introgressed from the wild Mexican hexaploid Solanum demissum ended in abject failure. With the advent of facile gene mapping and cloning, allied to knowledge of plant resistance gene structure, renewed efforts are leading to mapping and isolation of new sources of late blight resistance in potato wild species, many of which are being performed under the auspices of the BIOEXPLOIT project (Sub-project 2). We document recent advances in late blight resistance gene mapping and isolation, and postulate how these genes, allied to knowledge of pathogen effectors and their recognition specificity, may greatly enhance our chances of halting the progress of late blight disease in potato crops worldwide.     

General resistance against potato virus Y introduced into a commercial potato cultivar by genetic transformation with PVYN coat protein gene

Summary Transgenic cv. Folva potato plants expressing the coat protein gene of potato virus Y strain N (PVY^N) were produced usingAgrobacterium tumefaciens mediated transformation. Forty independent transformants were selected for resistance screening. Four clones showed complete resistance to mechanical inoculation with all the five PVY isolates tested: the PVY^N isolate from which the coat protein gene was derived, two PVY^O isolates, and two PVY^NTN isolates. Two of the fully resistant clones contained only one copy of the transgene, demonstrating that it is possible by genetic engineering to obtain highly virus resistant potato clones that can also be useful in future breeding programmes.     

Potato germplasm collecting expedition to the Guaitecas and chonos Archipelagos,Chile, 1990

Summary A joint Chilean, Italian, and United States potato (Solanum tuberosum) germplasm collecting expedition was conducted in the Guaitecas and Chonos Archipelagos, south of Chiloé Island, between March 4 – March 21, 1990. The expedition resulted in 30 collections ofSolanum tuberosum and 1 collection ofFragaria chiloensis L. Twenty-three of the potato collections were along the salt-water-swept shores of the islands. These beach populations, unlike the indigenous landraces in southern Chile, are self-perpetuating populations and provide useful new germplasm for researchers interested in the origin of cultivated potatoes and in the origin ofSolanum tuberosum in Chile.     

Societal Costs of Late Blight in Potato and Prospects of Durable Resistance Through Cisgenic Modification

In the European Union almost 6 Mha of potatoes are grown representing a value of close to €6,000,000,000. Late blight caused by Phytophthora infestans causes annual losses (costs of control and damage) estimated at more than €1,000,000,000. Chemical control is under pressure as late blight becomes increasingly aggressive and there is societal resistance against the use of environmentally unfriendly chemicals. Breeding programmes have not been able to markedly increase the level of resistance of current potato varieties. New scientific approaches may yield genetically modified marker-free potato varieties (either trans- and/or cisgenic, the latter signifying the use of indigenous resistance genes) as improved variants of currently used varieties showing far greater levels of resistance. There are strong scientific investments needed to develop such improved varieties but these varieties will have great economic and environmental impact. Here we present an approach, based on (cisgenic) resistance genes that will enhance the impact. It consists of five themes: the detection of R-genes in the wild potato gene pool and their function related to the various aspects in the infection route and reproduction of the late blight causing pathogen; cloning of natural R-genes and transforming cassettes of single or multiple (cisgenic) R-genes into existing varieties with proven adaptation to improve their value for consumers; selection of true to the wild type and resistant genotypes with similar qualities as the original variety; spatial and temporal resistance management research of late blight of the cisgenic genetically modified (GM) varieties that contain different cassettes of R-genes to avoid breaking of resistance and reduce build-up of epidemics; communication and interaction with all relevant stakeholders in society and transparency in what research is doing. One of the main challenges is to explain the different nature and possible biological improvement and legislative repercussions of cisgenic GM-crops in comparison with transgenic GM-crops. It is important to realize that the present EU Directive 2001/18/EC on GM crops does not make a difference between trans- and cisgenes. These rules were developed when only transgenic GM plants were around. We present a case arguing for an updating and refinement of these rules in order to place cisgenic GM-crops in another class of GM-plants as has been done in the past with (induced) mutation breeding and the use of protoplast fusion between crossable species.