Novel Fusarium Wilt Resistance Genes Uncovered in the Wild Progenitors and Heirloom Cultivars of Strawberry

Abstract

Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria × ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and wild octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here we show that resistance to both races is widespread and that resistance to race 1 is mediated by dominant genes (FW1, FW2, FW3, FW4, and FW5) on three non-homoeologous chromosomes (1A, 2B, and 6B). The resistance proteins encoded by these genes are not yet known; however, plausible candidates were identified that encode pattern recognition receptor or other proteins known to mediate gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

A medium‐density genotyping platform for cultivated strawberry using DArTag technology

“…The recent availability of high‐quality reference genomes and sequence datasets for strawberry has provided essential resources for trait mapping, functional genomics, and genetic marker development in this allo‐octoploid hybrid species (Bassil et al., 2015; Edger et al., 2019; Hardigan et al., 2020, 2021; Lee et al., 2021; Hardigan et al., 2021; Mao et al., 2023; Shirasawa et al., 2021). The growing molecular breeding toolbox for strawberry has nevertheless needed cost‐effective high‐throughput marker genotyping solutions to enable genomic selection and routine forensic identification of individuals and parents on a large scale (Gezan et al., 2017; Jiménez et al., 2023; Osorio et al., 2021; Pincot et al., 2020, 2021; Whitaker et al., 2020). MIP‐like technologies offer the advantages of high sample throughput and the ability to sequence target amplicon regions at a high read depth, reducing the likelihood of missing genotypes or genotyping errors at heterozygous sites (Wang et al., 2023).…”

“…(2020). The publication of multiple single nucleotide polymorphism (SNP) arrays for strawberry from 2015 to 2020 enabled genetic and physical mapping of new loci controlling traits related to disease resistance and fruit quality (Bassil et al., 2015; Barbey et al., 2021; Castillejo et al., 2020; Jiménez et al., 2023; Noh et al., 2018; Nelson et al., 2021; Nellist et al., 2019; Oh et al., 2019; Osorio et al., 2021; Oh et al., 2021; Pincot et al., 2018, 2020, 2021, 2022; Pillet et al., 2017; Petrasch et al., 2022; Salinas et al., 2019). Progress in this area has only increased following the publication of multiple high‐quality, chromosome‐scale assemblies of octoploid Fragaria genomes in the last 5 years (Edger et al., 2019; Hardigan et al., 2021; Lee et al., 2021; Mao et al., 2023; Shirasawa et al., 2021).…”

Why is usefulness rarely useful

“…Our work focuses on strawberry, another outbred, clonally propagated species, at the University of California Davis (UCD) strawberry breeding program. This breeding program is currently investing in infrastructure to implement genomics data in breeding decisions (Pincot et al 2022;Jiménez et al 2023;Hardigan et al 2023;Feldmann et al 2023;Knapp et al 2024) and has detailed records of the pedigrees of current varieties which help evaluate the success of the statistical models necessary for predicting usefulness (Pincot et al 2021;Knapp et al 2023;Feldmann et al 2024) as detailed below.…”