Lee Chaehee, Epstein Lynn, Kaur Sukhwinder, Henry Peter M, Postma-Haarsma A Dorien, Monroe J Grey, Van Deynze Allen
Department of Plant Sciences, University of California, Davis, California, 95616, USA.
Department of Plant Pathology, University of California, Davis, California, 95616, USA.
Plant J. 2025 Jun;122(5):e70251. doi: 10.1111/tpj.70251.
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.
芹菜（Apium graveolens var. dulce）的生产可能会受到真菌病原体尖孢镰刀菌芹菜专化型（Foa）的限制，尤其是在温度高于22°C时。由于芹菜的遗传基础狭窄，一种芹菜种内杂交品种被培育成了“挑战者”品种，它对引起镰刀菌黄化病的Foa小种2具有抗性，但对引起镰刀菌枯萎病的相对不相关病原体Foa小种4敏感。我们构建了一个高质量的、染色体水平的“挑战者”品种物理图谱，其中包含3.3 Gbp的40464个基于RNA的蛋白质编码基因模型，并将其与遗传图谱进行了锚定。尽管染色体末端基因密度高且重组率更高，但平均每个染色体56%的基因位于重组率较低的区域（<0.025 cM/Mb）。我们鉴定了“挑战者”品种的核苷酸结合和富含亮氨酸重复序列受体（NLRs）以及模式识别受体（PRRs），这两个基因家族编码了大多数抗性（R）基因。在三个处理组（模拟侵染或用Foa小种2或小种4侵染）中，通过Quant-Seq 3' mRNA-Seq（Tag-Seq）对芹菜冠部的243个NLRs和445个PRRs进行了定量分析。我们将“挑战者”品种的基因组与之前发表的中度易感Foa小种2的“文图拉”品种的基因组进行了比较。我们提出了一个用于芹菜基因组辅助育种的工具箱，其中包括注释的基因模型、一种简化基因组测序的方案、NLRs和PRRs表达的记录，以及一种将选定的NLR超级簇渐渗的直接策略，其中高达83%的NLR超级簇位于重组率较高的区域。
