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

Fusarium wilt, a vascular disease of strawberry (Fragaria <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:semantics><mml:mo>×</mml:mo> <mml:annotation>$\times$</mml:annotation></mml:semantics> </mml:math> 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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:msub><mml:mi>S</mml:mi> <mml:mn>1</mml:mn></mml:msub> <mml:annotation>${\mathrm{S}_{1}}$</mml:annotation></mml:semantics> </mml:math> progeny segregated 15 resistant:1 susceptible ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:msup><mml:mi>χ</mml:mi> <mml:mn>2</mml:mn></mml:msup> <mml:mo>=</mml:mo> <mml:mn>0.03</mml:mn> <mml:mo>;</mml:mo> <mml:mi>p</mml:mi> <mml:mo>=</mml:mo> <mml:mn>0.87</mml:mn></mml:mrow> <mml:annotation>$\chi ^2 = 0.03; p = 0.87$</mml:annotation></mml:semantics> </mml:math> ), 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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:msub><mml:mi>S</mml:mi> <mml:mn>1</mml:mn></mml:msub> <mml:annotation>${\mathrm{S}_{1}}$</mml:annotation></mml:semantics> </mml:math> 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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:msub><mml:mi>S</mml:mi> <mml:mn>2</mml:mn></mml:msub> <mml:annotation>${\mathrm{S}_{2}}$</mml:annotation></mml:semantics> </mml:math> 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.