Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.

中文翻译：

---

在亲本基因组从头组装的支持下，对甜瓜重组自交系群体中的早熟性和果实成熟性状进行 QTL 作图和基因组分析。


早熟和成熟行为是葡萄树上和葡萄下果实的重要属性，影响着种植者和消费者的质量和偏好。水果成熟是一个复杂的生理过程，涉及影响水果颜色、硬度和香气产生的代谢变化。甜瓜是研究果实成熟的有前途的模型作物，因为更年期行为的全谱在自然变化中得到体现。使用源自亲本系“Dulce”（网状，更年期）和“Tam Dew”（inodorus，非更年期）的重组自交系（RIL）群体，其早熟性和成熟性状各不相同，我们绘制了乙烯排放、果实硬度的 QTL以及开花和成熟的天数。为了进一步注释主要QTL区间并识别候选基因，我们使用Oxford Nanopore长读长测序结合Illumina短读长重测序，从头组装亲本基因组。除了在亲本之间检测到的 250 万个全基因组 SNP 和短 InDels 之外，我们还在此强调了这些品系与参考甜瓜基因组之间的结构变异。通过系统的多层优先排序过程，我们鉴定了多性状 QTL 内候选基因的 18 个潜在多态性。选定的 SNP 与早熟性状和成熟性状的关联在 177 个不同的甜瓜品种和源自 20 个不同亲本的核心子集的 190 个 F1 杂种的双列基因群体中得到了进一步验证。先进的基因组工具与不同的种质和目标绘图群体的结合被证明是一种利用正向遗传学策略来剖析复杂的园艺重要性状的方法。