Enhancing the sustainability of fresh-market snap bean production in the Northeast by identifying and promoting cultivars with tolerance to Cucumber mosaic virus (CMV).

Final Report for GNE10-007

Project Type: Graduate Student
Funds awarded in 2010: $15,000.00
Projected End Date: 12/31/2012
Grant Recipient: Cornell University
Region: Northeast
State: New York
Graduate Student:
Faculty Advisor:
Dr. Phillip Griffiths
Cornell University
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Project Information

Summary:

Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV), Clover yellow vein virus (ClYVV) and other aphid-transmitted viruses have caused significant economic damage to snap bean production in New York State, and the Northeast region of the United States since 2001. The most effective, efficient, and ecologically sensitive means to reduce the damage caused by CMV, BYMV, and ClYVV is to identify or develop, and to deploy of resistant and/or tolerant cultivars. In pursuit of this objective, we assembled and evaluated 217 snap bean cultivars for symptom expression and symptom severity response to CMV and BYMV, and 94 snap bean cultivars for response to ClYVV. While no cultivars were resistant to CMV or BYMV, they varied widely for the severity of disease symptoms expressed. A subset of cultivars with divergent symptom expression was selected for simultaneous field-based testing of the impacts of CMV and BYMV on yield, and for identifying cultivars with potential tolerance to yield loss. In addition, five previously unrecognized cultivars were identified as resistant to the ‘New York’ strain of ClYVV. Once adopted, the results from this project should help to reduce the economic damage caused by aphid-transmitted viruses to snap bean production in the Northeast region of the United States.

Introduction:

The purpose of this project is to enhance the prospects for sustainable production of fresh-market snap bean (Phaseolus vulgaris L.) production in New York State and the Northeast by identifying and promoting snap bean cultivars that maintain acceptable levels of yield when infected with Cucumber mosaic virus (CMV, family Bromoviridae, genus Cucumovirus). Snap beans are an important vegetable crop in the Northeast region of the United States, particularly in New York State, where the total production area and value rank second in the country (USDA NASS 2010). In 2008, snap bean growers in New York harvested 6,600 acres of fresh-market snap beans with a farm-gate value of 40.5 million dollars (USDA NASS 2010). In 2009, 6,700 acres of fresh market snap beans were harvested with a farm gate value of approximately $23.5 million dollars (USDA NASS 2010). A total yield decline of 45% in 2009 as compared to 2008 can be largely attributed to severe CMV pressure during the 2009 season (Reiners 2010).
A disease complex incited by aphid-transmitted viruses has caused substantial economic damage to the yields and quality of snap bean production in a number of Northeastern states including New York and Pennsylvania since 2001 (Larsen et. al 2002). The increase in virus disease incidence and severity has been associated with the increasing prevalence of the soybean aphid (Aphis glycines Matsumura), an introduced and efficient vector of CMV (Gildow et al. 2008). While the sampling of virus-infected fields has revealed the presence of a number of distinct viruses including Alfalfa mosaic virus (AMV, family Bromoviridae, genus Alfamovirus), Bean yellow mosaic virus (BYMV, family Potyviridae, genus Potyvirus), and Clover yellow vein virus (ClYVV, family Potyviridae, genus Potyvirus) among others, CMV is the most prevalent virus detected (Tolin and Langham 2010). CMV has the potential to infect up to 100% of the plants in a field (Larsen et. al. 2002, Shah et al. 2006, Nault et al. 2006), and it may have the potential to cause yield losses ranging from 5-60% (Taylor and Shail 2006).
Few options exist to control the epidemics and associated crop damage caused by CMV and other aphid transmitted viruses. The use of pesticides to control the aphid vectors of CMV and other aphid-transmitted viruses is ineffective, as the soybean aphid does not colonize snap bean. Clearly the most effective, efficient, and ecologically sensitive control strategy is to develop cultivars with resistance to the viruses. Unfortunately, no snap bean cultivars appear to be completely resistant to CMV infection. Snap bean cultivars do however exhibit significant variation in the severity of symptoms as well as the severity of yield loss in response to CMV infection (Hart and Griffiths (unpublished); Taylor and Shail (2006)). Consequently, the evaluation of the response to CMV infection in a diverse representation of snap bean cultivars will better characterize the relationship between the patterns of symptom expression and yield loss and will better document the impact of CMV infection on the yield of snap beans in the Northeast. Most importantly, it will help to identify snap bean cultivars capable of producing acceptable yields when infected with CMV.

Relevance to Sustainable Agriculture

The identification and promotion of fresh-market snap bean cultivars that are capable of maintaining acceptable yields when infected with CMV contributes directly to the overall goal of protecting and enhancing the capacity of agriculture in the Northeast to be both diversified and profitable while providing healthful products to its consumers. Fresh-market snap beans are an important crop to diversified producers in the Northeast given their relatively early maturity and flexibility in crop rotation, their relatively high value, and the ubiquitous consumer preference for this nutritious vegetable. In addition, fresh-market snap bean production takes place on a large number of diversified farms of all sizes, particularly on relatively small, family-owned farms scattered throughout the entirety of the Northeast region (USDA NASS 2010). The project has considerable potential for meaningful and widespread impact in reducing the yield losses caused by CMV and potentially other viruses in the Northeast.
The impact of CMV on the yield of snap beans in the Northeast has not been completely characterized nor addressed, particularly in the context of fresh-market snap bean production. Previous publications (Reiners 2010, Taylor and Shail 2006), though informative, have not been undertaken nor published in the context of the rigor required for peer-reviewed scientific publication. Though this does not necessarily detract from their potential utility and impact, it does signal the need for more in-depth research. In addition, given the major importance of the consolidated snap bean industry in New York, previous efforts have focused on a narrow range of snap bean cultivars that are targeted to the processing industry. The many small and diversified farms of the Northeast that produce snap beans for the fresh-market have a much smaller demand for seed and a much more flexible demand for a diverse range of snap bean cultivars. The proposed project seeks to serve the interests of the fresh-market producer by evaluating a much larger and more diverse set of snap bean cultivars, and by publishing and publicizing the results as widely as possible.

Project Objectives:

The objectives remain identical to the original plan of work except that they have been expanded. The final objectives are listed below followed by a brief description of what has been accomplished to date.

Objective 1

Characterize symptom expression in response to infection by Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV), and Clover yellow vein virus (ClYVV) in a diverse group of snap bean cultivars

Objective 1 has been completed. This objective motivated a thorough examination of the natural genetic variation available in snap beans for symptom expression in response to infection with important aphid-transmitted viruses (CMV, BYMV, ClYVV) of the Northeast. The panel of snap bean germplasm was expanded to include 217 snap bean cultivars with relevance due to varying origins, dates of release, market classes, and potential virus resistance. The panel also now encompasses the 150 snap bean cultivar panel used for research by the bean research community and the USDA-NIFA funded Common Bean Coordinated Agricultural Project (BeanCAP). All 217 cultivars were evaluated for symptom expression and symptom severity responses to CMV and BYMV, and a subset of 94 cultivars were evaluated for their response to ClYVV in two replications (for complete results, see Electronic Supplementary Material 1 (ESM 1)). The evaluations were highly successful based on the efficiency of inoculation (near 100%), pronounced and repeatable symptoms on all known susceptible controls and cultivars, and no symptoms evident in uninoculated controls. A symptom severity index was developed that allowed for rapid and repeatable assessment of symptoms (see caption, Table 1). As expected, there was a wide range of symptoms in response to CMV, and BYMV, with less variation in response to ClYVV (ESM 1). Symptom severity in response to CMV and BYMV varied from very mild to very severe, and this allowed for the identification of snap bean cultivars with repeatable divergent symptom expression (ESM 1, Table 1). A subset of 18 cultivars with divergent symptoms both CMV and BYMV was assembled for the field-based evaluation of Objective 2. One barrier to greater success was obtaining and/or producing an adequate quantity of seed of the most interesting genotypes for both greenhouse and field-based testing within the time frame. Because of this, the selection of the 18 cultivars that were studied further was based somewhat more on availability than specific attributes. Nonetheless, the 18 cultivars represent a wide range of symptom expression and market classes, and are generally available in the seed trade. The evaluation of a subset of 94 cultivars for response to ClYVV ultimately lead to the identification of 5 previously unrecognized snap bean cultivars with resistance to the ‘New York’ strain of ClYVV (ClYVV-NY) (Table 2). This impact of these results will be discussed under section 6 ‘Impact of Results’.

Objective 2

Conduct field-based evaluation of the response to infection with CMV, BYMV, and ClYVV in a subset of snap bean cultivars with diverse symptom expression in order to:

-(2a.) Determine the impact of CMV, BYMV, and ClYVV infection on the yield of snap bean cultivars with a range of symptom expression.

-(2b.) Characterize the relationship between patterns of symptom expression and yield loss.

-(2c.) Identify snap bean cultivars capable of producing acceptable yields when infected with CMV, BYMV, and ClYVV.

The order of sub-objectives 2b and 2c has been changed to better represent how the data will be used. The data collection for Objective 2 has been completed. The data analysis and synthesis required for completing Objectives 2a, 2b, and 2c is ongoing. This objective proved to be considerably difficult to accomplish as reported in the annual reports for 2010 and 2011. In addition, because of the labor involved in the data collection methods used in 2011 (harvesting dry pods and seeds from 1600 plants by hand), a small subset was collected and analyzed, and subsequently deemed not worth the expense and effort to acquire. The harvest itself was highly variable due to a high percentage of incomplete pod filling and effects of late season disease on plants, seeds, and pods. Nonetheless, a new approach to the experimental design, adjusted methodology and labor requirements, and renewed effort was applied to attempt to complete the data collection for Objective 2 during the 2012 growing season. Because most scientific journals require that results be repeated at least once, the goal became to plan and execute two separate experiments in two separate environments (separated by one month between sowing dates). Two separate sets of experiments, as outlined in section 4 ‘Materials and Methods’, were executed and all data was collected by October 1, 2012. The data is still currently in an analysis and synthesis phase, but it appears to have generated a data set of clear significance and interest.

Objective 3

Publish and Disseminate Results

Objective 3 has yet to be completed in full, but a manuscript that addresses all of Objective 2 is in preparation. The barrier to accomplishing Objective 3 was the overall difficulties encountered in the project that lead to significant delays in accomplishing Objective 2. The identification of the five ClYVV resistant snap beans (Table 2) as the result of Objective 1 has been incorporated into a manuscript that details parallel research on the molecular genetics of resistance to ClYVV in common bean (Hart and Griffiths (submitted)). A field day presentation of the project (see ESM 2) was made to the Cornell University (CU) Vegetable Breeding Institute (a public/private partnership in vegetable breeding) and preliminary results were recently shared with the Snap Bean Advisory Council of the New York State Vegetable Research Association (NYSVRA).

Cooperators

Click linked name(s) to expand
  • Dr. Phillip Griffiths

Research

Materials and methods:

The approach and overall design of the project was based on the attempt to identify an appropriate experimental design and set of methodologies to efficiently accomplish the goals of Objective 1 and 2 for this project, and for the sake of the overall research effort of snap bean breeding and genetics lead by Dr. Griffiths at Cornell. The goals of Objective 1 were achieved efficiently and adequately by the materials investigated and the methodology presented in previous reports. The barriers to efficiently accomplishing the goals of Objective 2 were mainly the availability of enough high quality seed for the extensive replication required of a randomized split plot design. The level of replication necessitated that only a few cultivars could be entered, and that the effects of only one virus could be estimated. These barriers were overcome by adapting an augmented split-plot experiment design (ASPED) where the cultivars were assigned to the whole plots, and virus infection status (+/-) was assigned to the sub-plots (ESM 2). The commercial ‘check’ cultivars were arranged as a randomized complete block design (RCBD) and then the block size was increased in order to include four additional new or ‘augmented’ treatments (cultivars) in each block, each appearing only once in the experiment. Augmented experiment designs were developed for screening large numbers of genotypes or other treatments and they provide a way of adjusting the yields of the augmented cultivars for block-to-block differences as well as providing an estimate of experimental error and an objective way of comparing the augmented cultivars with the check cultivars (Federer and King 2007). The experimental methodology for the execution of the field experiments was otherwise identical to the methodology described in previous reports.

Research results and discussion:

The majority of the results and accomplishments have been outlined in section 3 ‘Objectives/Performance Targets’. Although the project did not develop exactly as planned, and required that significant course corrections be made along the way, it was in most cases a success.

Research conclusions:

The project has provided meaningful opportunities to explore the relevance of my research and to attempt to translate the results of my research to the field. The project planning, execution, and outreach components of the project provided direct experience in grant-funded project management that isn’t available to all graduate level researchers. I see the development of my character and capacity in research as being a very important impact of the project.
The project has now assembled and characterized a particularly relevant panel of snap bean germplasm for symptom expression in response to CMV, BYMV, and ClYVV infection. The characterization has demonstrated that although no snap bean cultivars are resistant to CMV or BYMV, they do vary significantly in their response to virus infection and in how they express symptoms, which is valuable information for both growers and particularly those involved in serving growers through snap bean cultivar development. While there are major sources of resistance to these viruses outside of the snap bean gene pool, and this resistance is being introgressed into snap bean through CU breeding efforts, this project allowed for the exploration and assessment of additional genetic variation for response to virus infection. Although this variation is still being explored and assessed, it may have an important impact as it may lead to a more durable or useful level of tolerance and/or resistance to CMV and BYMV. This avenue would likely not have been explored if not the context of the project. In addition, the project has developed a platform for efficient and effective future research in this area. This platform, and the experience gained through the implementation of the project will help to propel future effort in this area.
The identification of five previously unrecognized snap bean cultivars with resistance to ClYVV is an important impact, as these cultivars could be promoted immediately to stakeholders. These cultivars also served an important role in supporting a hypothesis and providing materials for research validation in parallel research efforts on the molecular genetics of ClYVV resistance in common bean (Hart and Griffiths (submitted)).
It is anticipated that the data generated from the experiments implemented in 2012, and possibly beyond, will eventually lead to accurate and objective information on which cultivars may be best to grow in snap bean production areas that experience aphid-transmitted virus epidemics. It is hoped that such information will help to enhance the sustainability of snap bean production in the Northeast by reducing the crop damage caused by prevalent viruses.

Participation Summary

Education & Outreach Activities and Participation Summary

Participation Summary

Education/outreach description:

The identification of the five ClYVV resistant snap beans (Table 2) as the result of Objective 1 has been incorporated into a manuscript that details parallel research on the molecular genetics of resistance to ClYVV in common bean (Hart and Griffiths (submitted)). A field day presentation of the project (see ESM 2) was made to the Cornell University (CU) Vegetable Breeding Institute that was attended by more than 30 public and private sector vegetable breeders. Preliminary results were also recently shared with the Snap Bean Advisory Council of the New York State Vegetable Research Association (NYSVRA). Overall the outreach objectives have been effective despite the difficulties with the project. ESM 3 presents overview images of the research undertaken in 2012.

Project Outcomes

Project outcomes:

Depending on the finalized results of all of the project data, the potential may exist to include some form of economic analysis in the data analysis and discussion. The analysis could include estimates of the potential economic impact of the three prevalent viruses on snap bean yield and income. Such estimates could also lead to potentially approximating the value of resistance and/or tolerance to yield loss. This is being considered and will be pursued should the data present the possibility.

Farmer Adoption

See section 6 ‘Impact of Results/Outcomes’

Assessment of Project Approach and Areas of Further Study:

Areas needing additional study

Additional experiments to obtain additional data on the impact of the viruses on the yield of snap beans, and to confirm any cultivars identified as tolerant should be carried out. Controlled environment evaluation of this impact and tolerance to infection would be informative. In addition, the inheritance of symptom expression in response to infection should be elucidated should this be meaningful in terms of protecting against yield loss. Populations have been constructed to investigate the genetics of mild versus severe symptom expression in response to virus infection. The development of an expanded snap bean diversity panel of 380 cultivars should be pursued and the panel should be phenotyped for response to CMV, BYMV, ClYVV, and numerous other virus species and strains. The panel may then allow for an association mapping approach to identify the major genes underlying many important virus resistances in common bean.

Literature Cited
  • Federer WT, King F (2007) Augmented split plot experiment design. In Federer WT, King F (eds) Variation on Split Plot and Split Block Experiment Designs. John Wiley & Sons, Inc. pp 169-187

    Gildow FE, Shah DA, Sackett WM et al. (2008) Transmission efficiency of Cucumber mosaic virus by aphids associated with virus epidemics in snap bean. Phytopathol 98: 1233-1241

    Hart JP, Griffiths PD (2010) Differentiation of aphid-transmitted viruses in snap beans using reverse transcription polymerase chain reaction. Annu Rep Bean Improv Coop 53:98-99

    Hart JP, Griffiths PD (submitted) A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean. Theor Appl Genet

    Hart JP, Griffiths PD (201_) The response of snap bean cultivars to infection with some prevalent viruses of the Great Lakes Region of the United States. (In preparation for submission to Plant Disease)

    Larsen RC, Miklas, PN, Eastwell KC et al. (2002) A virus disease complex devastating late season snap bean production in the Midwest. Proc Bean Improv Coop 45:36-37.

    Nault BA, Shah DA, Taylor, AG (2006) Viruses and aphids everywhere in New York snap bean fields in 2005, pp. 74-76. In Proceedings of the 2006 Empire State Fruit and Vegetable EXPO. February 13-16, 2006. Cornell Coop Exten, Syracuse, NY.

    Reiners S, (2010) 2009 A tough year for NY vegetable growers. Online Publication. Cornell Coop Exten (http://www.vegetables.cornell.edu/PDF/2009_value.pdf)

    Shah DA, Dillard HR, Mazumdar-Leighton S et al. (2006) Incidence, spatial patterns, and associations among viruses in snap bean and alfalfa in New York. Plant Dis 90:203-210

    Taylor AG, Shail, JW (2006) The impact of CMV in reducing yield of selected snap bean cultivars. Annu Rep Bean Improv Coop 49:199-200

    Tolin SA, Langham MAC (2010) Virus surveillance in beans using tissue blot immunoassay: three years experience of the Legume IPM-PIPE. Annu Rep Bean Improv Coop 53:52-53

    United States Department of Agriculture National Agricultural Statistics Service (USDA-NASS) (2010) Washington, DC. http://quickstats.nass.usda.gov/. Accessed 23 May 2010

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.