Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.

结构变异（SV）是重要的作物改良和驯化性状的基础。然而，解决 SV 的范围、多样性和定量影响一直具有挑战性。我们使用长读长纳米孔测序捕获了 100 个不同番茄品系中的 238,490 个 SV。这个 panSV 基因组以及 14 个新的参考组件揭示了不同基因型的大规模混合，以及数千个交叉基因和顺式调控区域的 SV 。数百个 SV 基因对表现出微妙而显着的表达变化，这可能广泛影响数量性状变异。通过将定量遗传学与基因组编辑相结合，我们展示了改变基因剂量和表达水平的多个 SV 如何改变水果的风味、大小和产量。在最后一个例子中，影响三个相关转录因子的四个 SV 之间的高阶上位性允许在现代番茄中引入重要的收获性状。我们的研究结果强调了 SV 在基因型与表型关系中尚未得到充分研究的作用及其在作物改良中的广泛重要性和效用。