Biological Sciences, University of Southampton, Southampton, United Kingdom.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA.
Mol Biol Evol. 2019 Jul 1;36(7):1359-1372. doi: 10.1093/molbev/msz062.
In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.
在食品安全的背景下，研究驯化的基因组学将有助于识别适应和具有经济重要性的表型的基因，例如更大的果实、改善的味道和失去农艺上较差的表型。对基因组规模的单核苷酸多态性的研究证明了茄子（茄子）野生祖先之间的关系，确认了 Solanum insanum L. 是野生祖先。该物种大致分为东部（马来西亚、泰国和越南）和西部（印度、马达加斯加和斯里兰卡）两个群体，其驯化种来自前者。来自印度的其他“野生”品种似乎是野生逃逸种，通过与驯化品种的杂交多次衍生而来。果实较小的卵形品种通常与东亚 Solanum insanum 混在一起，这表明它们与大果的驯化品种相比是原始的。比较转录组学用于追踪选择下的基因座。序列分析表明，与野生种相比，原始品种的遗传瓶颈使变异减少了近 50%，与地方品种相比又减少了 10%。我们还证明了与创伤和细胞凋亡反应有关的基因选择的证据。在野生和原始品种之间或原始品种和地方品种之间表达差异显著的基因在衍生种群中大部分（>75%）下调，并富集了与防御、开花、信号转导以及对生物和非生物刺激的反应相关的基因本体论。这项工作揭示了参与作物驯化和改良的基因组变化，群体遗传学工作解释了为什么定义茄子驯化轨迹如此具有挑战性。
