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Abstract Detail



Genomics / Proteomics

Liu, Jun-jun [1], Sniezko, Richard [2], Murray, Michael [3], Wang, Ning [4], Sturrock, Rona [1], Zamany, Arezoo [1], Kegley, Angelia [2], Savin, Douglas [2].

Transcriptome profiling reveals whitebark pine genetic diversity for resistance to white pine blister rust.

Whitebark pine (WBP, Pinus albicaulis) is one of the pioneer species and has many ecological benefits in high-elevation forests in North America. This wide-ranging species provides valuable contributions to watershed protection, wildlife habitat, food source for several species. WBP stands are, however, vulnerable to several environmental disturbances, including white pine blister rust (WPBR) caused by exotic fungus Cronartium ribicola, mountain pine beetle, fire suppression, and climate change. WPBR has killed about 50% of WBP trees in the Rocky Mountains, up to 85 to 95% of the stands in some high pathogen hazard areas since its arrival in the early 20th century. As a result, WBP is listed as endangered by the Committee on the Status of Endangered Wildlife in Canada and has been designated ‘warranted, but precluded’ in the U.S. under the Endangered Species Act. Therefore, disease resistance screening programs have been undertaken in Canada and in the United States to determine the frequency and levels of resistance and their potential utility for conservation and restoration of this endangered species. No major gene has as yet been identified, but families differing remarkably in resistance have been identified in artificial inoculation trials. The resistance appears to have a number of components, notably resistant families showing a lower percentage of seedlings with stem infections, latent stem infections, bark reactions and ability to tolerate or survive longer with stem infections. In general, less than 1% of all whitebark pines are rust resistant. Traditional breeding may benefit from advanced genomic technologies and novel marker-assisted selection approaches. In the present genomics study, genetic variations in terms of resistance to WPBR were investigated by RNA-seq-based transcriptome profiling and high-throughput genotyping of single nucleotide polymorphisms (SNPs). A collection of WBP germplasm from British Columbia was used for construction of cDNA libraries in RNA-seq analysis. Approximately one billion 2 x 100-bp reads were obtained from vegetative organs (needles, stems, and roots) of two-year-old seedlings and de-novo assembly generated the WBP transcriptome containing >300,000 unique transcripts. Bioinformatic SNP detection identified >100,000 high quality SNPs among BC seed-families. To find SNP markers useful for WBP breeding conservation, 120 seed-families collected across western North America were genotyped. The latest analysis results on association of SNP markers with quantitative disease resistance will be presented and application of WBP SNP markers will be discussed. The WBP transcriptome database and those validated SNP markers provide novel genomic resources for genetic, evolutionary and ecological studies.


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1 - Canadian Forest Service, Natural Resources Canada, Pacific Forestry Centre , 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
2 - USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
3 - Ministry of Forests, Lands and Natural Resource Operations, #401 - 333 Victoria St., , Nelson, BC, V1L 4K3 , Canada
4 - Qinghai University, Academy of Agriculture and Forestry Science, 253 Ningda Road, Xining, Qinghai, 810016, China

Keywords:
Genetic resistance
RNA-Seq
Transcriptome
SNP genotyping
whitebark pine
white pine blister rust.

Presentation Type: Oral Paper:Papers for Topics
Session: 48
Location: Salon 19/20/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 4:00 PM
Number: 48010
Abstract ID:164
Candidate for Awards:None


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