PLANT-SIDE PROJECTS

Analysis of the genetic basis of plant quantitative disease resistance

     The basis of multigenic quantitative disease resistance in plants is poorly understood, but such resistance is well known for its track record of durability in agricultural production environments. In collaboration with several other labs we are working to dissect the genetic and mechanistic bases of single and multiple disease resistance in maize.

With respect to multiple disease resistance, we have found population-based evidence (QTL co-localization, genetic correlations, and gene-phenotype associations) of gene clusters and pleiotropy for disease resistances in rice and maize. We are isolating disease QTL in near-isogenic germplasm that can be used for detailed analyses (e.g. physiological, histological, etc.) on the basis of resistance.

Collaborating labs: Kirk Czymmel (UD), Peter Balint-Kurti (USDA-ARS, NCSU), Jim Holland (USDA-ARS, NCSU), Gary Payne (NCSU), Rebecca Nelson (Cornell), Nick Lauter (USDA-ARS, ISU), Alicia Carriquiry (ISU)

Funding (includes collaborator sources): National Science Foundation, USDA-AFRI, CGIAR Generation Challenge Program, and NCCorn Growers Association.

Development and implementation of a genetic framework for studying response to artificial selection

     Selection is fundamental to breeding. To better understand responses to selection, we are developing a genetic framework that allows for the identification of selected QTL and quantification of allele frequency shifts at those QTL. This combined approach is being developed in collaboration with Jim Holland (USDA-ARS, NCSU) and Peter Balint-Kurti using a maize population improved by Marty Carson (USDA-ARS, Univ. Minnesota) for quantitative resistance to northern leaf blight. Earlier work (under the guidance of R. Nelson) was conducted in collaboration with S. Murray (TAMU) to develop an empirical-based test statistic to identify loci responsive to artificial selection.

Funding: The National Research Initiative of the USDA Cooperative State Research, Education, and Extension Service project 2007-35301-18133

Analysis of environmental adaptation: photoperiodism in maize

     Photoperiodism represent a genetic barrier to adapting plants to new environments and confounds assessment of the true genetic merit of potentially valuable germplasm. In maize, a short-day species, tropical germplasm often exhibits sensitivity to the longer daylengths that occur at latitudes away from the equator. This sensitivity causes a delay in plant maturity that increases with increasing daylengths. Because maturity is correlated with most other traits, it is not possible to accurately assess the value of alleles in their target production environments.

     We are using our approach for dissecting the genetic architectureof response to selection to study environmental adaptation. Arnel Halluer (Iowa State Univ.) conducted a decade of selection for earliness to adapt a tropical landrace (Tusón) to central Iowa. Collaborating with Jim Holland (USDA-ARS, NCSU), Sherry Flint-Garcia (USDA-ARS, Univ. Missouri), Nick Lauter (USDA-ARS, Iowa State Univ.), Natalia de-Leon (UW Madison), Seth Murray (TAMU), and Wenwei Xu (TAMU), we have phenotyped samples from different generations of selection across a latitudinal transect spanning from Wisconsin to Puerto Rico. We are now in the process of genotyping this material to allow for our combined approach to be applied. This project is aimed at characterizing the genetic architecture of response to selection and providing information that would aid in the use of alleles from tropical maize.

Funding: USDA-AFRI; project website: http://www.maizeatlas.org

Genomic resources development for breeding and gene discovery in lima bean

     Lima bean (Phaseolus lunatis) is Delaware's signature crop; Delaware is a leader in lima bean production. Despite its importance to the state, almost no genomic resources are available for lima bean improvement. In state-funded projects, our lab is working with Dr. Tom Evans and Emmalea Ernest to develop molecular markers for use in lima bean breeding. In this initiative, we are working on the development of a method for marker discovery and genotyping for species with no reference genome. The genotyping-by-sequencing method is applicable to any species and we are developing the method in collaboration with Keith Hopper (USDA-ARS, UD) who is applying it to study insect genetics.

Funding: Delaware Department of Agriculture

FUNGAL-SIDE PROJECTS

Analysis of naturally occurring variation in fungal pathogenesis to plants

     The natural variation underlying fungal pathogenesis is virtually uncharacterized. The maize/Cochliobolus heterostrophus pathosystem—the interaction between maize and the fungus C. heterostrophus that causes Southern Leaf Blight disease—is unique in that both the plant host and microbial pathogen are genetically tractable organisms. Maize is a model species for studying quantitative genetics. C.heterostrophus is a model species for studying pathogenesis. We are laying the groundowrk for studying quantitative variation in C.heterostrophus. We are currently developing high-throughput population development techniques and phenotypic assays using diverse fungal strains provided by collaborator Gillian Turgeon (Cornell). Ultimately, combining traditional fungal genetics with quantitative genetic analysis will provide a very powerful approach to understand natural pathogen variation.

Funding: UD Research Foundation