Two HCS faculty members receive big grants in Plant Breeding!

Dec. 12, 2014

Two Horticulture and Crop Science faculty members, Dr. David Francis and Dr. Clay Sneller, received two grants from the United States Department of Agriculture. The grants were part of the FY 2014 AFRI Plant Breeding Projects. The FY 2014 AFRI plant breeding projects focus on public breeding efforts to improve crop yield, efficiency, quality and/or adaptation to diverse agricultural systems and includes:

  • Pre-breeding and germplasm enhancement, cultivar development, selection theory, applied quantitative genetics, and participatory breeding;
  • Development of tools to predict phenotype from genotype to accelerate breeding of finished varieties; or
  • Conference grants to identify regional needs for plant breeding research, educatio,n or extension.

The plant breeding program was very competitive this year, with only 5% of proposals receiving funding.  Of the 9 proposals funded, two were in the Department of Horticulture and Crop Science. 

Read the full press release here:


Brief descriptions of the grant proposals are below. 


INVESTIGATOR: Francis, D. M.; Mutschler-Chu, MA.

NON-TECHNICAL SUMMARY: This research addresses seeks to merge resistances developed by separate breeding programs in New York and Ohio in order to control a complex of diseases that affect tomato health and fruit quality. We will develop complementary sets of fresh market and processing tomato lines possessing naturally occurring resistance to the five most important diseases of field grown tomatoes in the North East, Atlantic Coast and Midwestern U.S.: bacterial spot, bacterial speck, Septoria leaf spot, early blight and late blight. By combining resistance, releasing public germplasm, and making available key DNA-based genetic marker information, we can improve fruit and foliar health and reduce pesticide use in tomatoes grown in humid regions. Enhancing crop plant health and production requires that we address complex sets of problems in an integrated fashion rather than only one problem at a time. As an outcome we will generate both key plant material and efficient methodologies for their use. The advances in tomato breeding and genetic research in the past five years, including the release of a draft genome sequence, leave us well positioned to address the problem of combining multiple resistance across market classes of field-grown tomatoes. During the course of the proposed studies we will compare two breeding approaches, background genome selection and genome wide selection in order to assess the relative efficiency of the methods based on gain under selection, time, and cost. This work will provide a model for other vegetable breeding efforts.

OBJECTIVES: The specific goals of this project are:Objective 1. Use marker assisted selection (MAS) to select for recombination events that bring 3 genes for control of Septoria leaf spot, bacterial speck, & bacterial spot into coupling phase (Chromosome 5). Objective 2. Use marker assisted selection (MAS) to generate a set of near isogenic lines containing different subsets of three genes/QTL on Chromosome 11 that provide resistance to multiple species of Xanthomonas.Objective 3. Use background genome selection and genome wide selection methods to combine resistance to multiple diseases into elite germplasm for processing and fresh market tomato.Objective 4. Release the resulting lines and information through multiple existing channels for use by private and public tomato breeders/geneticists, plant pathologists, and other researchers





NON-TECHNICAL SUMMARY: Genomic selection (GS) is a relatively new crop breeding strategy for complex traits. Empirical results from training populations and cross-validations show the great potential of GS to improve the annual rate of gain. Genomic selection can affect many aspects of a population that impact breeding efficiency including trait values, allele frequencies, diversity, and linkage disequilibrium (LD). Genomic selection is now being adapted by many breeders and it imperative to assess the impact of multiple cycles of GS on trait improvement and genome structure. This knowledge could be used to develop breeding strategies that enhance the efficiency of GS by accentuating positive changes and negating negative ones. The goal of breeding for a complex trait is often to make an undefined incremental improvement. Data used to implement GS can also be used to develop more concrete goals, develop strategies to achieve the goals, and monitor progress. For example, GS models could be used to estimate the maximum trait value a population could produce and to pick parental pairs and breeding method that provide the best probability of obtaining the maximum value.Overall Hypothesis:Genomic selection will affect traits and other aspects of the wheat genome and GS models and data can be used to develop efficient breeding strategies.Specific objectives:1) determine the impact of five cycles GS on target traits and breeding values (GEBV), 2) Assess impact of GS on the wheat genome 3) Assess GS strategies to obtain a target trait value, 4) develop criteria to pair parents to provide the best probability of obtaining a target value.Potential impact and expected outcomes: The research will help breeders decide whether to use GS and how best to implement GS. Our assessment of the impact of GS on genome structure can be used to determine population size, number and which crosses to make, strategies to offset the negative effects of drift, strategies to maintain diversity, and the extent and persistence of negative and positive linkage blocks and how to deal with them. Coupling GS with early generation breeding strategies designed to improve the efficiency of attaining defined goals will produce a greater probability of success and will improve the effectiveness of all subsequent breeding activities and resources.

OBJECTIVES: 1) Determine the impact of up to five cycles Genomic Selection (GS) on target traits and breeding values (GEBVs). 2) Assess the impact of GS on the diversity, allele frequencies, and linkage disequilibrium. 3) Develop genomic breeding strategies to design crosses to attain defined goals and utilize family selection.