Transcriptome Mining and Targeted Resequencing Identifies Candidate Fusiform Rust Resistance Genes in Loblolly Pine

Fr genes control resistance to fusiform rust in loblolly pine. Candidate Fr genes encode NLR proteins. We combined a transcriptome mining approach with targeted resequencing to identify novel NLR genes and map SNPs that reliably segregate with rust resistance. We mined the transcriptomes of rust-resistant pine families to identify novel NLR genes. We next designed probes to target novel NLR genes as well as regions of interest in the loblolly pine reference genome assembly. We used our probes to resequence progeny in a loblolly family segregating for a specific resistance gene, Fr1, and identified SNPs that segregated with the resistance phenotype in the loblolly pine family.