Genomics study of western white pine (Pinus monticola) genetic resistance against white pine blister rust

Abstract

Western white pine (WWP, Pinus monticola) is a long-lived conifer with an extensive geographic range in western North America. It is of high interest in ecological studies and forest breeding because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola). However, P. monticola lacks genomic resources and is evolutionarily far away from plants with available draft genome sequences. Use of high-throughput RNA-sequencing (RNA-seq) technology is a costeffective strategy to generate substantial transcriptome data for global transcript profiling and DNA marker discovery. We report here the RNA-seq analysis results using Illumina® (San Diego, California, USA) deep sequencing of P. monticola infected with C. ribicola. De novo gene assembly was used to generate the first P. monticola consensus transcriptome of primary needles, which contained 39,439 unique transcripts with an average length of 1,303 bp and a total length of 51.4 Mb. About 23,000 Pinus orthologous genes (POGs) and 200 disease resistance gene analogs (RGAs) encoding NBS-LRR proteins were identified by BLAST search against the Pinus gene index database and plant R gene families, respectively. Comparison of transcriptomes from WPBR-susceptible and -resistant white pine genotypes revealed about 1,000 differentially expressed genes (DEGs) with statistical significance during early stages of the compatible and incompatible P. monticola-C. ribicola interactions.

Parent Publication

• Proceedings of the IUFRO joint conference: Genetics of five-needle pines, rusts of forest trees, and Strobusphere; 2014 June 15–20; Fort Collins, CO

Citation

Liu, J.-J.; Sniezko, R. A. 2018. Genomics study of western white pine (Pinus monticola) genetic resistance against white pine blister rust. In: Schoettle, Anna W.; Sniezko, Richard A.; Kliejunas, John T., eds. Proceedings of the IUFRO joint conference: Genetics of five-needle pines, rusts of forest trees, and Strobusphere; 2014 June 15-20; Fort Collins, CO. Proc. RMRS-P-76. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. p. 113.