Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A “bottom-up” population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low π for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.

中文翻译：

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使用转录组数据识别茄子驯化过程中的目标基因组区域

识别在驯化过程中发生分化的基因和性状为维持甚至增加现有作物的产量和营养提供了重要的关键信息。“自下而上”的群体遗传学方法被用来识别整个茄子基因组的选择特征，以更好地了解驯化过程。获得了 4 个野生茄子 (Solanum insanum L.) 和 16 个驯化茄子 (S. melongena L.) 的 RNA-seq 数据，并映射到茄子基因组。在驯化中表现出选择特征的单核苷酸多态性 (SNP) 被确定为在 2 个种群之间表现出高 FST（显着分歧的证据）和驯化种群的低 π（表明选择性扫描）。其中一些区域似乎与先前确定的驯化性状数量性状基因座重叠。针对拟南芥和番茄基因组搜索了围绕这些 SNP 的连锁不平衡区域中的基因，以找到直系同源物。随后的基因本体（GO）富集分析确定了与光合作用和对环境的反应相关的 GO 术语的过度表示。这项工作揭示了茄子驯化和改良所涉及的基因组变化，以及这与观察到的番茄基因组变化的比较，揭示了参与这两个物种驯化的共享染色体区域。随后的基因本体（GO）富集分析确定了与光合作用和对环境的反应相关的 GO 术语的过度表示。这项工作揭示了茄子驯化和改良所涉及的基因组变化，以及这与观察到的番茄基因组变化的比较，揭示了参与这两个物种驯化的共享染色体区域。随后的基因本体（GO）富集分析确定了与光合作用和对环境的反应相关的 GO 术语的过度表示。这项工作揭示了茄子驯化和改良所涉及的基因组变化，以及这与观察到的番茄基因组变化的比较，揭示了参与这两个物种驯化的共享染色体区域。