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Home → Publications → Tree Improvement and Genetics → Southern Forest Tree Improvement Conference → 35th Southern Forest Tree Improvement Conference (2019) → Identification of Candidate Interacting Resistance and Avirulence Genes in the Fusiform Rust Pathosystem

Identification of Candidate Interacting Resistance and Avirulence Genes in the Fusiform Rust Pathosystem

Fusiform rust is a disease incited by the fungus Cronartium quercuum f.sp. fusiforme (Cqf) on southern pines (where it causes galls on stems and branches) and on oaks (where it causes minimal leaf damage). Fusiform rust is a major disease threat to the timber industry in the US. Rust galls cause yield losses that exceed US$100M/year. A high priority for breeders and forest managers is to identify candidate resistance genes in loblolly pine (Pinus taeda L.; P. taeda) and avirulence genes in Cqf. However, identifying the specific loci that regulate phenotypic traits in conifers is a major undertaking because of their very large genomes. During the process of annotating the genome of P. taeda, an expressed sequence tag (EST) was identified that contains a single nucleotide polymorphism (SNP) mapping to Fusiform rust resistance locus 1 (Fr1), which interacts with the Cqf gene, Avirulence locus 1 (Avr1). This EST aligns to a transcript from RNA-sequencing data and a TIR-NB-LRR protein, thus identifying it as a candidate Fr1 gene. Here we present the results of work mapping Fr1 in the Pinus taeda genome and Avr1 in the Cronartium quercuum genome. We conducted bulk segregant analysis of next-generation sequence data from both host and pathogen. In pine, half-sibling progeny from a resistant mother were phenotyped as either resistant or susceptible to Cqf. These progeny were sequenced with a custom sequence-capture method targeting a genomic region linked to resistance by prior work. In Cqf, analysis of whole-genome sequence of rust grown on resistant or susceptible seedlings identified a 200kbp region containing several likely effector proteins. By identifying candidates for an interacting avirulence and resistance gene pair in this conifer-rust pathosystem, we will discover markers that will guide breeding and deployment of resistant pine.


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Author(s): Daniel Ence, Katherine E. Smith, Amanda L. Pendleton, Thomas L. Kubisiak, Claire L. Anderson, Asaf Salamov, Andrea Aerts, Robert W. Riley, Alicia Clum, Erika A. Lindquist, Nicolas Feau, Robin Paul, Braham Dhillon, Michael C. Campbell, Zev Kronenberg, Igor Grigoriev, Mark Yandell, Richard C. Hamelin, Matias Kirst, Leandro Neves, Jill Wegrzyn, C. Dana Nelson, John M. Davis

Publication: Tree Improvement and Genetics - Southern Forest Tree Improvement Conference - 2019