USDA-SCRI Project

USDA Specialty Crop Research Initiative (SCRI)

Welcome to
Cucumber Applied Genomics Project Website!

Project Title:¬†Translational Genomics in Cucumber¬†–
Tool Development & Application for Recessive Disease Resistances

(USDA NIFA CRIS Project Number: 2011-51181-30661)

Background Information
Objectives of Project
Participants
Industry Participants

Background Information

Cucumber (Cucumis sativus L.) is an important specialty crop in the United States. In 2008, cucumber ranked 4th in total acreage (151,720 acres) among the 20 major vegetable crops, with a total farm-gate value of $421 million (2008 USDA Agriculture Statistics). Unfortunately, cucumber yield has been stagnant for more than two decades. In recent years, there has been an increase in consumer demand for cucumber fruit, yet cucumber growers face new challenges such as heightened international competition and increased production costs, due mainly to the significant increase in the cost of oil and its byproducts and increased disease, pest, and environmental pressure that reduce fruit yield and quality.

A recent national survey among stakeholders (Weng, 2009) identified downy mildew (DM) and viruses as major challenges to US cucumber production. Down mildew is caused by the oomyceteous pathogen Pseudoperonospora cubensis and incites major losses worldwide. In the past 40 years, the use of resistant cultivars successfully controlled DM on cucumber in the U.S. However, in 2004, a new destructive strain of DM caused serious epidemics, and has become the primary threat to US cucumber production (Colucci et al. 2006). For example, Michigan is the leading state for pickling cucumber production (38,000 acres with finished product value of $240.7 million in 2008). Since 2005, Michigan has witnessed annual epidemics of DM. Frequent fungicide sprays (i.e., every 5 days) are required to control this disease, placing significant economic pressure on cucumber growers. In 2006, Michigan growers and processors suffered over $6.4 million losses due to this disease. In North Carolina, one of the leading slicing cucumber producing states, acreage has declined since 2004 due to the high cost of fungicides to control DM. DM continues to spread throughout the US, and is now becoming a problem even in southern California (Drotleff 2009).

While DM is re-emerging as a threat, viruses have been a persistent problem of all major cucurbit crops. The most damaging viruses in cucumber include Zucchini yellow mosaic virus (ZYMV) and other potyviruses such as watermelon mosaic virus (WMV) and the watermelon strain of Papaya ringspot virus (PRSV-W). Infection of ZYMV promotes propagation of other viruses such as Cucumber mosaic virus on the same cucumber plant (Wang et al. 2004; Zeng et al. 2007). During an epidemic, virus pathogens are often very difficult to control. Although resistances are known for cucumber viruses, development of multiple virus resistant varieties is not easy due to the recessive nature of resistances.
In comparison with many field crops, cucumber genetic and genomic resources have been very limited. However, with recent advances in technology and instrumentation for sequencing plant genomes, this situation has rapidly changed. The whole genomes of three cucumber lines recently have been sequenced. Over 4 million cucumber ESTs have been generated. Hundreds of SSR markers have been developed from the whole genome sequences. These resources are providing new opportunities to expedite traditional plant improvement through molecular marker-assisted breeding. However, there is still a large translational gap between utilization of these genomic sequences and field-based breeding. This USDA-SCRI project aims to developing applied genomics tools to address two critical issues in cucumber production: resistances to DM and potyviruses. To this end, we will develop a high throughput SNP genotyping platform, a high-resolution genetic map, and a functional genomic system for assay of candidate genes. These tools are important not only for molecular mapping or cloning of DM and potyvirus resistance genes; they will also be indispensable for many other applications in molecular breeding studies.

Objectives of Project

1. Develop a suite of translational genomics research tools including:

– A SNP array for high throughput genotyping;

– An integrated genetic-physical map to facilitate genetic mapping, gene cloning and marker-assisted selection;

– A virus-induced gene silencing (VIGS) platform for gene function assay.

2. Identify and utilize molecular markers for incorporation of recessively inherited resistance gene(s) to the new DM strain; as well as map-based cloning of the resistance locus zym associated with multiple potyvirus resistances;

3. Explore molecular plant-pathogen interactions to understand mechanisms of evolving virulence in the DM pathogen;

4. Evaluate economic benefits of disease resistances on commercial production of cucumber;

5. Develop an effective outreach plan to educate our stakeholders on benefits of modern molecular technologies in cucumber breeding, and actively engage them for quick delivery of results from this project.

Participants

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Dr. Yiqun Weng (PD)
USDA-ARS Vegetable Crops Research Unit
Horticulture Department,
University of Wisconsin – Madison, WI 53706
Email: yiqun.weng@wisc.edu

Dr. Rebecca Grumet (co-PD)
Department of Horticulture,
Michigan State University, East Lansing MI 48824
Email: grumet@msu.edu

Dr. Michael Havey (co-PD)
USDA-ARS Vegetable Crops Research Unit
Horticulture Department,
University of Wisconsin – Madison, WI 53706
Email: michael.havey@ars.usda.gov

Dr. Todd Wehner (co-PD)
Department of Horticultural Science,
North Carolina State University, Raleigh, NC 27695,
Email: todd_wehner@ncsu.edu

Dr. Brad Day (co-PD)
Department of Plant Pathology,
Michigan State University, East Lansing, MI 48824
Email: bday@msu.edu

Dr. Steven Miller (co-PD),
Center for Economic Analysis,
Michigan State University, East Lansing, MI 48824
Email: mill1707@msu.edu

Dr. Bernard Zandstra (co-PD)
Extension Specialist, Department of Horticulture,
Michigan State University, East Lansing, MI 48824
Email: zandstra@msu.edu

Curtis Talley Jr. (Collaborator)
Extension Farm Management Educator,
Michigan State University Extension, East Lansing, MI 48824
Email: talleycu@msu.edu

Industry Participants (non-federal match fund providers)

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east west seeds

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nunhems

magnumseedhead