Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

• The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed.
• To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of Helianthus annuus, as well as two cross-compatible wild relatives, H. argophyllus and H. petiolaris.
• Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped QTLs, such as branching. Admixture analyses revealed that all of the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line.
• Cumulatively, introgressions cover approximately 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes likely because of the re-introduction of branching.

• 现代作物的培育通常兼具人工选择与杂交两种手段，但迄今为止绝大多数相关研究仅聚焦于前者。本研究旨在探究这两类过程及其交互作用，如何塑造了作为全球重要油料作物的栽培向日葵的基因组。
• 为鉴定向日葵驯化与改良过程中受人工选择靶向作用的基因，并检测其与野生近缘物种在驯化后的杂交渐渗事件，本研究对80份基因型材料的转录组序列进行了分析，样本涵盖野生普通向日葵（Helianthus annuus）、地方品种以及现代栽培品系，同时纳入两个杂交亲和的野生近缘种：银叶向日葵（H. argophyllus）与叶柄向日葵（H. petiolaris）。
• 异常值分析共鉴定出122个与驯化相关的候选基因，以及15个与改良相关的候选基因。与此前多项研究结果一致，推测参与油脂生物合成的基因呈现最为显著的异常值特征。此外，本研究还观测到多个与已定位数量性状基因座（QTL, Quantitative Trait Locus）相关的潜在关联，其中包括分枝性状。群体混合分析结果显示，本次分析的所有现代栽培品种基因组均携带至少一处来自野生种群的渐渗片段，且每条染色体在至少一个现代品系中均存在渐渗证据。
• 综合来看，渐渗片段总计覆盖栽培向日葵基因组约10%的区域。令人意外的是，渐渗片段并未避开候选驯化基因，这一现象大概率与分枝性状的重新引入有关。