Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

Tania Quesada,Matias Kirst,Patricio Muñoz,Salvador Gezan,Jill Wegrzyn,Gary Peter,Marcio Resende Jr,C Nelson,David Neale,John Davis

doi:10.3390/f5020347

Abstract

Fusiform rust resistance can involve gene-for-gene interactions where resistance (Fr) genes in the host interact with corresponding avirulence genes in the pathogen, Cronartium quercuum f.sp. fusiforme (Cqf). Here, we identify trees with Fr genes in a loblolly pine population derived from a complex mating design challenged with two Cqf inocula (one gall and 10 gall mixtures). We used single nucleotide polymorphism (SNP) genotypes at sufficient density to ensure linkage between segregating markers and Fr genes identifying SNPs that explained high proportions of variance in disease incidence using BayesCp, that also were significant using Bayesian Association with Missing Data (BAMD) software. Two SNPs mapped near Fr1 and generated significant LOD scores in single marker regression analyses for Fr1/fr1 parent 17 as well as four other parents. One SNP mapped near Fr8 and was significant for parent 28. Two SNPs mapped to linkage groups not previously shown to contain Fr genes and were significant for three parents. Parent 2 showed evidence of Fr gene stacking. Our results suggest that it is feasible to identify trees segregating for Fr genes, and to map Fr genes, based on parental analysis of SNPs that cosegregate with disease incidence in designed resistance screening trials.

Highlights

Fusiform rust is one of the most important pine diseases in the southeastern United States [1,2]
Individual single nucleotide polymorphism (SNP) explained a greater proportion of the variance for gall score than for gall length, as the top five SNPs for gall score accounted for 29.9% of the variance, whereas the top five SNPs for gall length accounted for only 4.3%
Because the SNPs declared by BAMD as significant represented a subset of the total number of SNPs detected by BayesC, we focused our attention on those SNPs that were detected by both methods

Summary

Introduction

Fusiform rust is one of the most important pine diseases in the southeastern United States [1,2]. It is caused by the fungus Cronartium quercuum (Berk.) Miyabe ex Shirai f.sp fusiforme (Cqf), which alternates between oak and pine host species [1]. In pine, this fungus causes galls in stems and branches, reducing growth, reducing wood quality and making trees susceptible to breakage in windstorms, thereby generating significant economic losses [2]. These are allele-specific interactions between host and pathogen—if the host is homozygous recessive (fr/fr) for an Fr gene, or if the pathogen carries an allele for virulence (avr) that can overcome the host Fr gene, the result in both cases is a diseased host

Results

Discussion

Conclusion