S1015: Host Resistance as the Cornerstone for Managing Plant-Parasitic Nematodes in Sustainable Agroecosystems (S-282)
Statement of Issues and Justification
Project's Primary Website is at http://www.uga.edu/srel/S-1014_Multi-State_Research_Project/index.html (direct link can be found under LINKS)The proposed project is requesting approval for 5 years due to the long term nature of plant breeding programs. It often requires more than 10 years from the discovery of a resistance gene until that gene is available to growers in agonomically acceptable cultivars. The first nematode resistance cultivars in peanut (Simpson and Starr, (2001), soybean, and tomato (Starr et al., 2002) took longer than 10 years from discovery to availability to the growers. It is expected that many cultivars and new sources of resistance will be released during the life of this project because of prior achievements in this direction. The proposed project will build on the successes in discovery, characterization, and develop of resistance made under the current S-282 project.
Plant-parasitic nematodes cause yield suppression in many crops species. The warm temperate to subtropical climates, abundance of favorable, coarsely-textured soils, and numerous susceptible crops all combine to make nematodes particularly important pathogens in the southern region of the United States. Among the crops with the greatest estimated losses due to nematode parasitism are cotton, cucurbits, leguminous vegetables, peanut, solanaceous vegetables, soybean, sugarcane, and tobacco (Koenning et al. 2000). Only alfalfa, hay, sorghum, rice, and wheat among the major crops were estimated to have losses of less than 1% of the yield potential. Nematode pathogens can be managed by application of various nematicides, by rotating to nonhost crops, by host resistance, and in some cases by biological control. Unfortunately, except for resistance, the use of these approaches is frequently not feasible on an economic basis due to low profit margins for most crops. There are a limited number of suitable nonhosts that can be rotated with the primary crop of interest in most cropping systems. Nematicides are costly and pose significant environmental and human health risks. There is a strong desire to further limit nematicide use. No new nematicide that has broad efficacy has been labeled for use in the past 25 years. The Food Quality Protection Act of 1996 will result in further restrictions on the use of nematicides and likely result in loss of registration for some (www.epa.gov/opppsps1/fqpa/). Increased use of host resistance to manage nematodes is attractive for several reasons. Resistance is an attractive option because it both protects crop yields from the damaging effects of nematode parasitism and resistance inhibits nematode development and reproduction (Roberts, 2002). Thus resistance, which can usually be used without any increase in production costs, also suppresses nematode population densities, and provides protection for subsequent susceptible crops.
The warm temperate to subtropical environment of the southern region of the United States enables plant-parasitic nematodes to complete multiple generations during the growing season. Additionally, in some cropping systems, winter survival is enhanced not only by the relatively mild winters of the region but also by the presence of susceptible hosts throughout the year. The southern region also has an abundance of coarsely textured soils that support the highest levels of nematode activity. Thus plant nematodes cause greater crop losses in the southern region than in any other region of the country.
The best documentation of these losses is for soybean (www.scnfact.org; www.ceris.purdue.edu/napis/pests/scn/facts.txt) and cotton (www.cotton.org/tech/pests/nematodes/losses.cfm). Soybean is susceptible to nine different nematode species, with the cyst nematode Heterodera glycines (SCN) being responsible for the greatest losses. SCN is present throughout the southern and midwestern states, and is found in a wide array of soils. The three root-knot nematodes (Meloidogyne arenaria, M. incognita, M. javanica ) are also widely distributed in all southern states and, whereas the distribution of these species is most common in the more coarsely textured soils, as a group they also cause substantial yield losses in soybean and many other crops. Other nematodes of more localize importance to soybean include the reniform nematode Rotylenchulus reniformis , the lance nematode Hoplolaimus columbus, lesion nematode Pratylenchus brachyurus, the stubby-root nematodes Paratrichodorus and Trichodorus, spp. and the sting nematode Belonolaimus longicaudatus. Among the other major crops of the region M. incognita and R. reniformis are important on cotton, M.arenaria is important on peanut, and all of the Meloidogynes species are important on several vegetable crops.
As indicated by the numerous stakeholders listed below that support the research efforts of one or more project participants, there is broad support of the ongoing efforts for the efforts of project personnel to develop additional sources of resistance to plant-parasitic nematodes in a large number of important crop species. These stakeholders consider the efforts to identify, characterize, and deploy host resistance to be of high priority. _______________________________________________________________________
Alabama Cotton Commission
Arkansas Soybean Promotion Board
Cotton Incorporated
Delta Pine and Land, Syngenta, and Paymaster Seeds
Florida Peanut Producers Association
Georgia State Support Program, Cotton Inc.
Georgia Agricultural Commodity Commission for Corn
Georgia Agricultural Commodity Commission for Peanut
Minnesota Soybean Research and Promotion Council
National Peanut Board
North Carolina Soybean Producers Association Inc.
North Carolina State Support Program, Cotton Inc
South Carolina Soybean Board
Tennessee Soybean Promotion Board
Texas Peanut Producers Board
United Soybean Board
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Consequences if research not completed.
Previously, plant-parasitic nematodes were controlled through the use of a variety of fumigant or non-fumigant nematicides (Whitehead, 1998). Availability of these pesticides has been increasingly restricted over the past 25 years due to increased federal regulation as concerns for human health and environmental safety increased. The Food Quality Protection Action (1996) is resulting in further restrictions on the use of nematicides. For example, the systemic nematicide phenamiphos will be withdrawn from all uses in the United States by corporate action by 2007 (personal communication, A. Lake, Bayer Crop Sciences). Additionally, because of the relatively limited market for nematicides (relative to herbicides and insecticides) and high cost of development, it is unlikely that new, safer nematicides will be developed in the near future. Thus, failure to make more effective use of currently available sources of resistance in sustainable cropping systems and to develop additional sources of host resistance will result in increased yield losses to producers as availability of nematicides declines.
Another concern relative to an over reliance on nematicides for management of nematodes is the failure of these pesticide to adequately control the pest population. Resistance to insecticides (Richter, 1992) and fungicides (Staub, 1991) in target pest populations is a well-documented phenomenon. No resistance to nematicides in populations of plant-parasitic nematodes has been documented outside of experimental, laboratory circumstances (Kampfe, 1995). However several instances of increased degradation of nematicides by soil microflora have been reported. These include the fumigant 1,3 dichloropropene (Ou et al., 1995), fenamiphos (Davis et al., 1993; Ou et al., 1994), and most recently aldicarb applied to cotton for control of reniform nematodes (McLean and Lawrence, 2003). Collectively, these three nematicides (aldcarb, 1,3-dichloropropene, and fenamiphos) are the most widely used nematicides in the United States. Continued reliance on such nematicides as may remain labeled, as opposed to development of more sustainable management systems, is likely to lead to additional incidences of nematicide failures due to increased rates of microbial degradation.
Although numerous soybean cultivars in a wide range of maturity groups are available that have resistance to a few races or species of H. glycines, Meloidogyne spp., and R. reniformis, this resistance is derived from relatively few genes. Thus, this resistance is vulnerable to virulence shifts in the nematode populations in response to selection pressures imposed by reliance on a limited number of resistance genes. Such shifts in virulence are well documented in the SCN/soybean system (Young and Hartwig, 1992). Of the species of root-knot nematodes that are responsible for substantial yield losses of peanut, M. arenaria has the greatest frequency distribution on peanut, but there are increasing finds of M. javanica parasitic on peanut and an as yet undescribed Meloidogyne species on peanut. Increased use of recently developed resistance to M. arenaria and M. javanica in peanut is likely to select for increased occurrence of other species as has been observed with tobacco after use of resistance to M. incognita became widespread (Fortnum et al., 1984). Currently available resistance to M. arenaria and M. javanica in peanut is due to a single dominant gene (Choi et al., 1999 ) and is available only in two cultivars that lack other necessary traits, especially resistance to the tomato spotted wilt virus (Starr et al., 2002 ). Additionally, currently there is no resistance in any peanut genotype to M. hapla, which is the most prevalent root-knot species in the NC/Va production region. The number of resistance genes available must be expanded and resistance introgressed in to a wider array of soybean and peanut cultivars. Failure to expand the numbers of resistance genes available to producers will result in increased yield losses with the development of nematode populations with virulence on currently available sources of resistance.
Cotton is the second most important crop of the southern region in terms of magnitude of losses due to nematodes. Based on data from regional surveys of nematode distribution and cotton response to nematicide treatments, total annual yield losses to the 15 million acre cotton crop have been estimated at $380 million for 2001 (Blasingame, 2002). The principal nematodes causing losses to cotton are the root-knot nematode M. incognita ($159 million in losses), which is widely distributed in all cotton production areas, and R. reniformis. Prior to the 1990's, the reniform nematode was considered a minor problem with most reports of crop losses from Louisiana and Mississippi. This nematode is now documented to be present throughout the southern region and in some areas of Alabama, Louisiana, and Mississippi is causing greater losses than M. incognita. The Columbia lance nematode (H. columbus) and the sting nematode (B. longicaudatus) are aggressive pathogens with more limited distributions than root-knot or reniform nematodes. Several sources of resistance are known for M. incognita in the cotton germplasm collection, and a few cultivars have been developed. However, the only currently available cultivar is the Acala-type NemX and it is not adapted to climates or production practices outside of Arizona and California. Resistance to R. reniformis is known in diploid Gossypium species (Robinson et al., 2003; Yik and Birchfield, 1984). However, genetic incompatibility represents a formidable barrier to introgression of these resistance genes into tetraploid cultivated cotton. Failure of the cotton industry to develop and use more resistance, as compared to the soybean and tobacco industries, is due to a number of factors. Chief among these are the perceived limited importance of nematodes relative to other pathogens and pests (Mueller et al., 1996), and the lack of effective, low cost, high through-put screening methodologies needed by commericial breeding programs. Failure to develop modern marker assisted selection protocols for nematode resistance will significantly delay development of nematode-resistant cultivars of cotton.
Technical Feasibility of proposed research.
The identification of resistance to numerous species of nematodes is a routine but time consuming task. Resistance is usually identified based on reduced levels of nematode reproduction on the resistant hosts relative to a susceptible host genotype (Roberts, 2002). Root-gall indices are a good measure of resistance to root-knot nematodes (Hussey and Jensen, 2002) but can be complicated by the presence of N-fixation nodules on peanut and soybean. Nodules can be mistaken for galls and thus plants with both galls and nodules require more time to evaluate, decreasing the efficiency of the system. Development of females and cysts (typically referred to as a female index) is often used to assess resistance to the soybean cyst nematode (Cook and Noel, 2002).
Marker-assisted selection (MAS) systems typically use one of several methods available for rapid detection of specific differences in DNA sequences between susceptible and resistant individuals (Young and Mudge, 2002). The several techniques (AFLP, RAPD, RFLP, SSR) are now routine at nearly all participating institutions, and in many of the laboratories of participating scientists. In the case of tomato, the resistance gene Mi-1 has been cloned and sequenced (Milligan et al., 1998 ), thus PCR primers that specifically amplify segments of the resistance gene can be used for MAS. With most other crops, the DNA sequence that is specific for the resistance loci is merely a sequence that is tightly linked genetically (ideally at a mapping distance of less than 5.0 cM) to the resistance locus. Such systems have already been developed for peanut (Church et al., 2002) and soybean (Young and Mudge, 2002); however, the peanut system is based on RFLP and needs additional research so that a more efficient system can be developed. Although no molecular markers linked to resistance in cotton have been reported, a molecular map of cotton has been developed (Rienisch et al., 1994) and can be used as a basis for identifying markers linked to resistance to root-knot nematodes. In cases where genetic data is more limited, techniques such as bulk segregant analysis (Michelmore et al.,1991) can be used to identify markers linked to resistance.
Need for cooperative work.
Currently, there are relatively few SY's devoted to plant nematology relative to the need. A coordinated, cooperative effort will increase the efficient use of these limited resources. A structure for cooperative work exists within the current S-282 Project, as demonstrated by the successful development of resistance in soybean, peanut and pepper. The proposed research on nematode resistance and how to most effectively integrate resistance with other control strategies and tactics can best be done by cooperation among the diminishing number of nematologists in the participating states and USDA ARS. Formal cooperation among participating scientists, through exchange of germplasm resources, avoidance of duplication of effort, and region-wide testing of new cultivars and cropping systems will increase the speed with which new technologies (resistance genes, resistant cultivars, MAS and cropping systems that incorporate a greater percentage of resistant crops) are developed and made available to appropriate clientele groups.
The current number of nematode-resistance genes available for introgression into cultivars is relatively small and thus these genes are vulnerable to virulence shifts in nematode populations and to shifts in predominant nematode species. There is a need to identify new resistance genes to ensure durability of the resistance phenotype. Project members will cooperate in this effort by dividing the effort in terms of germplasm resources being screened and relative efforts at characterization of sources of resistance. Cooperative efforts will ensure rapid and thorough examination of available germplasm collections for new and novel sources of resistance.
Most commonly grown cultivars or hybrids of soybean, cotton, and corn are developed in the private sector. Most of these private breeding companies depend on scientists from the land-grant universities and ARS to identify and characterize resistance genes. Further, most of these private companies lack the personnel and resources to effectively screen segregating breeding populations for resistance to multiple nematode species. Thus, there is an urgent need for development of DNA-based MAS systems, especially in cotton, peanut and several vegetable crops. Identification of molecular markers linked to resistance genes has been achieved in soybean and peanuts, however, some markers are based on RFLP and more efficient marker-assisted selection (MAS) systems are needed. MAS systems are needed that do not require use of 32P, but which are based on PCR technology for higher throughput (Young and Mudge, 2002). Refinement of existing MAS systems and expansion of the number of available markers will increase the ease with which private sector breeding programs can use available resistance genes. With private sector breeding programs assuming an increasingly important role in cultivar development, it is essential that we provide them not only with novel sources of resistance, but also with appropriate technology for introgression of these resistance genes into cultivars with the highest yield potentials. The communication and cooperation among participating scientists will ensure that the most urgent problems receive priority. With different laboratories focusing on different approaches (eg., RFLP, AFLP, RAPD, SSR) and different crop/nematode species systems, the greatest possible efficiency will be achieved.
Finally, scientists in cooperating states will evaluate resistant germplasm along with promising strategies for the integration of resistant cultivars with biological and (or) cultural control methods under a broad range of environmental conditions to determine how broadly (or narrowly) a particular gene or cropping system might be effective.
At annual research planning conferences, subcommittees organized around several research topics will meet to plan each years activities. These subcommittees will initially be orgainized around cotton, peanut, soybean, vegetables, and cropping systems. In the effort to identify new sources of resistance, the subcommittees will identify germplasm collections to be screened, intensity of screening activity, and division of effort. Similarly, once useful genes are identify, efforts to identify appropriate molecular markers will be similarly divided among the participating members such that no two participants are duplicating efforts but rather are concentrating on different resistance genes, or utilizing different approaches to identifying markers linked to the same gene. The cropping systems subcommittee will utilize a similar approach in design of experiments on optimal integration of resistance into sustaining cropping systems. Through this research planning effort, more effective use of limited SY's will achieve maximum progress across the broad objective of increased use of host resistance.
Likely impacts to be derived.
New vegetable, cotton, soybean, and peanut genotypes and cultivars that have durable resistance to multiple species and races of nematodes will result from the cooperative research. This resistance will allow the cultivars to achieve their genetic yield potential in fields infested with damaging population densities of plant-parastic nematodes. Resistance will be available to the growers with little or no increase in production costs and growers will be able to reduce use of costly and hazardous nematicides. Thus yields should increase with a decrease in production costs. Because resistance to nematodes typically results in a suppression of nematode reproduction, the lower nematode populations following a resistant crop will result in less nematode disease pressure on subsequent susceptible crops, as has been demonstrated in California for root-knot resistant cotton rotated with susceptible lima beans (Ogallo et al., 1999). Nematode control using nematicides typically provides only a temporary suppression of nematode population densities, such that nematicides must be applied annually. By expanding the number of crops with resistance and expanding the scope of resistance in those crops, fewer crops that support high levels of nematode reproduction will be grown.
Eleven soybean cultivars or germplasm lines with resistance to one or more nematode species, three cotton breeding lines with resistance to M. incognita, three pepper germplasm lines plus two pepper cultivars with resistance to M. incognita, one cowpea cultivar with resistance to M. incognita, and two peanut cultivars and one germplasm line resistant to M. arenaria and M. javanica were released by S-282 project personnel. The proposed regional effort will build on the successes of S-282 and result in a substantial increase in the number of resistance genes identified, introgression of those genes into appropriate crop genotypes, and development of cropping systems in which overall yield losses due to nematode parasitism are reduced.
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