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Seminar: Borrowing from Neighbors: Leveraging Comparative Genomics for Improved Plant Disease Resistance

Dr. James M. Bradeen, Professor and Department Head of the Department of Plant Pathology, Co-Director of the Stakman-Borlaug Center, University of Minnesota
Image: James Bradeen, University of Minnesota

Image: James Bradeen, University of Minnesota

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September 25, 2017, 3:35 PM - 4:30 PM

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Dr. Bradeen is a College of Agricultural Sciences Multicultural Diversity Fellow.

More information about James Bradeen

Abstract

Genetic disease resistance is a key component of crop production. Our research focuses on identifying, characterizing, and deploying genetic disease resistance. Across the globe, ~1,500 genebanks store crop plants and their wild relatives. These genebank collections are treasure troves waiting to be mined for traits useful for crop improvement. But traditional, phenotype-driven approaches to discover disease resistance genes, especially in crop wild relatives, have been slow and laborious, representing a bottleneck in crop improvement.

Across all plant species, approximately 75 percent of cloned disease resistance genes encode proteins of the nucleotide binding-leucine rich repeat (NB-LRR) superfamily. NB-LRR proteins act as sentinels and switches in plants, constantly on the lookout for pathogens (the role of sentinel) and activating resistance response as needed (the role of switch). NB-LRR genes evolve rapidly in response to pathogens, and plant genomes contain dozens to hundreds of NB-LRR genes. These characteristics have been impediments to comparative genomics approaches. In this study, we developed an informatics pipeline that allows comparison of NB-LRR genes across plant families.

Working in the Rosaceae, we have assembled a data set of nearly 2,500 NB genes from the genomes of 12 different species. Using a custom pipeline and a ‘diversity binning’ approach, we have collapsed computationally redundant diversity and completed phylogenetic analyses. Our results reveal nine ancient NB lineages that date to at least one hundred mya. As expected, NB gene representation varies substantially across plant species, but with few exceptions all NB lineages are represented across all species. Patterns of NB gene distribution reflects species phylogenies, with more closely related plant species sharing more NB lineages in common. Overall, our data reveal rapid rates of evolution at NB loci, consistent with variable and intense pathogen pressures. Intriguingly, a small number of NB genes are slow evolving and are shared across distantly related plant taxa. We hypothesize that patterns of NB diversification across plant species provides evolutionary clues to function, a hypothesis we are testing using the apple/apple scab (Venturia inaequalis) pathosystem. In the next phase of this project, we will optimize sequence-capture approaches to generate NB sequence data from genebank collections and species lacking reference genome sequences. Immediately applicable to marker assisted breeding for improved rose black spot (Diplocarpon rosae) resistance, this approach paired with our comparative informatics pipeline can reveal novel allelic diversity that can inform subsequent phenotypic testing—providing opportunity to rapidly identify useful NB-LRR alleles in genebank collections.

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814-865-7448