A well-annotated genome of Apium graveolens var. dulce cv. Challenger, a celery with resistance to Fusarium oxysporum f. sp. apii race 2.

Celery (Apium graveolens var. dulce) production can be limited by the fungal pathogen Fusarium oxysporum f. sp. apii (Foa), particularly at temperatures above 22°C. Because celery has a narrow genetic base, an intraspecific admixture of Apium graveolens was developed into cv. Challenger, which is resistant to Foa race 2, the causal agent of Fusarium yellows, but susceptible to Foa race 4, a relatively unrelated causal agent of Fusarium wilt. We assembled a high-quality, chromosome-level physical map of Challenger with 40 464 RNA-based, protein-coding gene models in 3.3 Gbp and anchored it with a genetic map. Although there is high gene density and higher recombination at the ends of the chromosomes, an average of 56% of the genes/chromosome are in lower recombination zones (<0.025 cM/Mb). We identified Challenger's nucleotide-binding and leucine-rich repeat receptors (NLRs) and pattern recognition receptors (PRRs), the two gene families that encode most resistance (R) genes. In three treatment groups (mock-infested or infested with either Foa race 2 or race 4), 243 NLRs and 445 PRRs were quantified in the celery crowns via Quant-Seq 3' mRNA-Seq (Tag-Seq). We compared the genomes of Challenger with that of the previously published cv. Ventura, which is moderately susceptible to Foa race 2. We present a toolbox for genome-assisted breeding for celery that includes annotated gene models, a protocol for genotype-by-sequencing, documentation of the expression of NLRs and PRRs, and a straightforward strategy for introgressing selected NLR superclusters, 83% of which are in higher recombination regions.