white pine pineconeWhite Pine Genome Project (WPGP)

There are nine white pines (also called five-needle or white pines) belonging to the genus Pinus sub-genus Strobus in North America that are vulnerable to attack by the exotic fungal pathogen Cronartium ribicola, causal agent of white pine blister rust (WPBR). WPBR has reached epidemic proportions in some species and is predicted to have catastrophic ecological consequences in others. Introduction of C. ribicola occurred on the east and west coasts in the early 1900’s and immediately had adverse effects on local forests. Recently, the incidence of WPBR has been recorded in pine populations in the great basin and the southwestern United States. Attempts to control WPBR with chemicals or by eradicating alternate hosts have been abandoned as impractical and ineffective.

Although C. ribicola is an introduced pathogen, heritable resistance has been observed in natural stands and under research conditions in several North American white pines. Resistance to WPBR falls into two categories. The first is major gene resistance (MGR) which is observed as a hypersensitive response (HR) and shown to be mediated by a single dominant gene that segregates in Mendelian fashion. Extensive genetic research has been conducted on this form of resistance in sugar pine (Pinus lambertiana) and western white pine (P. monticola) and is currently being conducted in limber pine (P. flexilis), southwestern white pine (P. strobiformis) and whitebark pine (P. albicaulis). It is not known if all white pines possess the capability for MGR. The current methodology for identifying resistant seedlings is time and labor intensive.

Little is known about the second form of resistance, which is broadly labeled partial resistance. Numerous disease expression patterns (i.e., slow-advance resistance, needle drop, ontogenic resistance) have been observed presenting infection symptoms that do not lead to mortality. The continuous distribution of disease phenotypes suggest that partial resistance is a complex trait controlled by few to several genes (polygenic).

Our research goals are to identify and isolate the genes that are responsible for conferring both types of resistance to WPBR. This work is being conducted in sugar pine because of the extensive resources accumulated for this species. DNA sequence technology for resistance genes would be efficacious in selective breeding and for monitoring forest health. Transfer of discovery and application to other members within the subgenus Strobus is anticipated.

White Pines Resequencing Project (WHISP)

The goal of this study is single nucleotide polymorphism (SNP) discovery in the North American members of the white pines (Pinus section strobus). These SNP’s will then be utilized to investigate evolutionary relationships among these species.

Primers for SNP discovery are a subset of those used for loblolly pine, validated on sugar pine. Approximately 200 genes will be assessed for a first pass in the following white pine species (with materials provided by the following people):

Species Institue
Pinus albicaulis Sierra Curtis-McLean, Andy Bower, USFS region 5 and 6.
Pinus aristata Anna Schoettle, Institute of Forest Genetics
Pinus ayacahuite Institute of Forest Genetics
Pinus balfouriana USFS Region 5
Pinus flexilis Anna Schoettle, Det Vogler, Institute of Forest Genetics
Pinus lambertiana Included in Comparitive Re-Sequencing in the Pinaceae Project
Pinus longaeva Det Vogler, Institute of Forest Genetics
Pinus monophylla Institute of Forest Genetics
Pinus monticola USFS Regions 5 and 6, BC Forest Service, IETIC
Pinus strobiformis Institute of Forest Genetics
Pinus strobus Natural Resources Canada, NC Forest Service, USFS Region 9

In addition, samples from a number of other Pinus section strobus species will be included as outgroups, for diversity panels, and to examine the genetic relationships among as many members of the section strobus as possible. Other species include, but are not limited to Pinus cembra, chiapensis, parviflora, koriainsis, armandii, wallichiana, pumila, peuce, sibirica, bungeana, gerardiana, morrisonicola, cembroides, edulis, maximartinezii, and pinceana.

SNP’s will be made available for public use following publication.

Participating Organizations

US Forest Service