# Whole‐genome sequencing bulked segregant analysis uncovered FW7, a Fusarium wilt resistance gene masked by epistasis in octoploid strawberry

## TL;DR

Researchers identified a new resistance gene (FW7) in strawberries that helps fight Fusarium wilt, a disease that causes plant death, and showed how it can be used with other genes to improve resistance.

## Contribution

The study uncovered a novel Fusarium wilt resistance gene (FW7) on chromosome 2A of octoploid strawberry, previously unreported for this trait.

## Key findings

- FW7 is a nearly additive resistance gene on chromosome 2A, masked by the epistatic effect of FW6.
- Whole-genome sequencing bulked segregant analysis (WGS-BSA) was validated for mapping resistance genes in octoploid strawberry.
- Highly predictive DNA markers for FW6 and FW7 were identified for marker-assisted selection.

## Abstract

Fusarium wilt, a vascular disease of strawberry (Fragaria
×
ananassa) caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. fragariae, has emerged over the past 20 years as a leading cause of severe plant wilt and death in California and many other parts of the world. We previously described several sources of resistance to race 1 of the pathogen; showed that resistance was conferred by dominant resistance genes (R‐genes) on chromosomes 2B (FW1, FW2, and FW5), 1A (FW3), and 6B (FW4); and identified a cultivar (Earliglow) that was hypothesized to be a source of novel R‐genes. Earliglow S1 progeny segregated 15 resistant:1 susceptible (χ2=0.03;p=0.87), the Mendelian distribution expected when the phenotypes are caused by unlinked dominant duplicate epistasis. Here, we show that Earliglow carries a dominant R‐gene (FW6) in the FW1 cluster on chromosome 2B and an incompletely dominant R‐gene (FW7) on chromosome 2A, where Fusarium wilt R‐genes have not been previously reported. The effect of FW7 was masked by the epistatic effect of FW6; this was determined by self‐pollinating an S1 individual predicted to be homozygous for the recessive (susceptible) FW6 allele and heterozygous for FW7 alleles, creating and whole‐genome sequencing Fusarium wilt resistant and susceptible S2 bulks, and physically mapping the FW7 locus by bulked segregant analysis. Lastly, we identified candidate genes for FW7, in addition to highly predictive FW6‐ and FW7‐associated SNPs for marker‐assisted selection of FW6 and FW7 alleles. This study laid the foundation for identifying the causal gene underlying FW7 and increasing the durability of resistance to Fusarium wilt by pyramiding FW7 with independent R‐genes.

The resistance of the heirloom cultivar Earliglow to Fusarium wilt race 1 is conferred by a dominant gene on chromosome 2B (FW6) and a nearly additive gene on chromosome 2A (FW7).The effect of FW7 was weaker than and masked by the epistatic effect of FW6.Whole‐genome sequencing bulked segregant analysis (WGS‐BSA) was validated as an approach for discovering and physically mapping DNA markers associated with large‐effect loci in octoploid strawberry.Highly predictive FW6‐ and FW7‐associated DNA markers were identified by genome‐wide association studies and WGS‐BSA.
FW6 and FW7 can be pyramided to increase the durability of resistance to Fusarium wilt race 1.

The resistance of the heirloom cultivar Earliglow to Fusarium wilt race 1 is conferred by a dominant gene on chromosome 2B (FW6) and a nearly additive gene on chromosome 2A (FW7).

The effect of FW7 was weaker than and masked by the epistatic effect of FW6.

Whole‐genome sequencing bulked segregant analysis (WGS‐BSA) was validated as an approach for discovering and physically mapping DNA markers associated with large‐effect loci in octoploid strawberry.

Highly predictive FW6‐ and FW7‐associated DNA markers were identified by genome‐wide association studies and WGS‐BSA.

FW6 and FW7 can be pyramided to increase the durability of resistance to Fusarium wilt race 1.

Fusarium wilt, a strawberry disease that causes wilting and death in susceptible genotypes, has become an increasingly serious problem in home gardens and farms around the world. There are, however, natural genetic sources of resistance to the causal pathogen (Fusarium oxysporum f. sp. fragariae), including wild relatives and heirloom and modern cultivars. We previously identified genes on three chromosomes (1A, 2B, and 6A) that confer resistance to the most common race of the pathogen found in California (race 1). Using insights gained from previous studies, we discovered that the heirloom cultivar Earliglow carries a novel race 1 resistance gene on chromosome 2A (FW7). The effect of this newly identified resistance gene was hidden by the epistatic effect of a dominant gene (FW6) found in a previously identified cluster of resistance genes on chromosome 2B. We uncovered and physically mapped FW7 using high‐throughput sequencing of resistant and susceptible bulks in combination with physical mapping of sequences to an octoploid reference genome, a tried‐and‐true approach known as bulked segregant analysis. Our study shows that strawberry has evolved multiple Fusarium wilt resistance genes that can be combined through marker‐assisted selection to prevent losses to the disease and increase the durability of resistance.