Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations.

Jun-Jun Liu,Angelia Kegley,Arezoo Zamany,Richard A Sniezko,Robert Sissons,Jodie Krakowski,Rachel A Zitomer,Genoa Alger,Holly Williams,Anna W Schoettle

doi:10.3389/fpls.2020.557672

Abstract

Since its introduction to North America in the early 1900s, white pine blister rust (WPBR) caused by the fungal pathogen Cronartium ribicola has resulted in substantial economic losses and ecological damage to native North American five-needle pine species. The high susceptibility and mortality of these species, including limber pine (Pinus flexilis), creates an urgent need for the development and deployment of resistant germplasm to support recovery of impacted populations. Extensive screening for genetic resistance to WPBR has been underway for decades in some species but has only started recently in limber pine using seed families collected from wild parental trees in the USA and Canada. This study was conducted to characterize Alberta limber pine seed families for WPBR resistance and to develop reliable molecular tools for marker-assisted selection (MAS). Open-pollinated seed families were evaluated for host reaction following controlled infection using C. ribicola basidiospores. Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola, MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4. These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola, including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). Interactions of associated loci were identified for MGR selection in trees with complex genetic backgrounds. SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. This work demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

Highlights

Limber pine (Pinus flexilis James) is a native five-needle pine in western North America, naturally distributed from British Columbia and Alberta in Canada to southern California in the USA
We aim to develop specific SNP markers that can be used for operational assays for Major gene resistance (MGR) selection in breeding programs of limber pine to increase the frequency of WPBRresistant genotypes
The present study documented MGR in three additional Alberta seed families as well as the previously identified PB #2, identifying new resistant germplasm to incorporate into the limber pine restoration program (Alberta Whitebark and Limber Pine Recovery Team, 2014)

Summary

Introduction

Limber pine (Pinus flexilis James) is a native five-needle pine in western North America, naturally distributed from British Columbia and Alberta in Canada to southern California in the USA. Because of the species’ high tolerance to drought, high winds, and exposure, individual trees can live for over 1,000 years in harsh environments where few other conifers are distributed In these environments limber pine provides essential ecosystem services, including slope stabilization, headwater streamflow control, and subalpine tree island formation. They provide cover that allows less exposure-hardy plants to establish and grow and provide both shelter and a nutritious food source for wildlife such as birds, bears, and small mammals (Schoettle, 2004; Tomback and Achuff, 2010). They are highly valued by recreationalists for their unique windswept beauty (Government of Alberta, 2014) and, as one of the world’s oldest living species, limber pine is useful for dendrochronological studies (Millar et al, 2007)

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