Combining resistances to major bacterial, fungal, and oomycete diseases of Northeast-adapted tomato

Project Overview

Project Type: Graduate Student
Funds awarded in 2017: $14,994.00
Projected End Date: 08/31/2019
Grant Recipient: Cornell University
Region: Northeast
State: New York
Graduate Student:
Faculty Advisor:
Dr. Martha Mutschler-Chu
Cornell University


  • Vegetables: tomatoes


  • Crop Production: plant breeding and genetics, varieties and cultivars
  • Education and Training: extension
  • Pest Management: genetic resistance
  • Production Systems: organic agriculture
  • Soil Management: soil quality/health
  • Sustainable Communities: sustainability measures

    Proposal abstract:

    Northeast fresh market tomato production is challenged by swift and severe outbreaks of the bacterial, fungal, and oomycete diseases bacterial spot (BLS), bacterial speck (BSk), early blight (EB), Septoria leaf spot (SLS), and late blight (LB). Favored by the ample rain, high humidity, and favorable temperatures of the Northeast, these foliar/fruit diseases reduce marketable yields, and reduce fruit quality. Growers, in turn, limit pathogen progress with multiple applications of copper (BLS, BSk) and/or fungicide (LB, EB, SLS). Effective genetic resistances are now available for each of these pathogens, but these resistance genes are not fully combined in “elite” commercial quality fresh market tomato lines. Recent advances in molecular marker technology, and background tomato breeding performed though a collaboration between Cornell and Ohio State, make the combination of all eight underlying resistance genes a reachable goal. This project will use these established resources to combine eight resistance genes to the five major diseases. Four bacterial resistance genes will be transferred to an elite Cornell fresh market tomato breeding line that already possesses four fungal resistance genes. Resulting lines will be field tested to determine acceptability of horticultural characteristics, and trials will be showcased to seed companies, extension staff, and regional growers. Superior lines will be released to seed companies for production of commercial hybrids with genetic control of multiple bacterial, fungal and oomycete diseases. Use of such hybrids would allow concurrent decreases in the use of chemical sprays, cost of production, and crop loss, while simultaneously increasing crop quality and profits.

    Project objectives from proposal:

    Objective 1:

    Use marker-assisted selection (MAS) and background genome selection to rapidly transfer BLS resistances (Rx-4 and QTL11; on chromosome 11) into well-adapted fresh market tomato breeding lines that already possess strong tolerance to EB (EBT) and resistances and LB (Ph-2 and Ph-3). Outcome: This is the first step to bringing BLS resistance into fungal resistant tomatoes. This Rx-4 and QTL11 “coupling phase” linkage provides broad resistance to BLS, but full control requires Rx-3 (on chromosome 5), which is added in objective 2.


    Objective 2:

    Use marker-assisted selection and background genome selection to rapidly transfer the BSk (Pto), BLS (Rx-3), and SLS (SLS-2) linked resistances on chromosome 5 into the same EB, LB, and BLS resistant tomato being produced in objective 1. Outcome: The combination of Rx-4, QTL-11, and Rx-3 provides the best resistance to all four species of Xanthamonas infecting tomato. The addition of Pto provides a valuable resistance to the primary race of Pseudomonas, race 0, causing BSk. The addition of Pto resistance to bacterial speck and the strongest current resistance to bacterial spot, in lines with genetic control of the major fungal/oomycete diseases of Northeast tomato, would provide an unprecedented level of disease control in fresh market tomato.

    Joint outcome:

    The combined results of objectives 1 and 2 will also produce a set of near-isogenic lines (NILs) containing different subsets of bacterial and fungal resistance genes/QTL in adapted fresh market tomato. These are valuable in breaking linkage drag, if present, and to plant pathologists studying interactions among resistance genes and pathogens.

    Objective 3:

    A) Field trial the lines and isolines created by objectives 1 and 2 to determine the acceptability of their horticultural plant/fruit type under low disease control input conditions, permitting the observation of natural infection. B) Also, perform laboratory tests of lines with/without BLS resistances (Rx-3 and QTL-11/Rx-4) to determine the degree of control possible in fresh market lines. Outcomes: Field trials will determine the impact of the chromosome 5 and 11 introgressions containing the bacterial resistance genes on the horticultural characteristics of the resulting lines. Characteristics include plant type, fruit size and quality, productivity and maturity. This will determine whether the transfer of either introgression also carries deleterious traits to be eliminated. BLS control will be assessed through laboratory assays and naturally infected field observation plots, both within this project, and by sharing seed with plant pathologists who routinely cooperate with Mutschler.

    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.