The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

中文翻译：

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对氮有效性的转录组反应揭示了四倍体小麦驯化过程中适应性可塑性的特征


作物的驯化，加上农业生态系统的发展，与重大的环境变化有关，并提供了表型可塑性的理想模型。在这里，我们检查了三个四倍体小麦 （Triticum turgidum L.） 亚种、野生 emmer、emmer 和硬粒小麦的 32 种基因型，它们代表了四倍体小麦驯化的关键阶段。我们开发了一个整合 RNA-Seq 数据和群体基因组学的管道，以评估基因表达可塑性并识别不同氮可用性条件下的选择特征。我们的分析揭示了初级 （野生 emmer 到 emmer） 和次级 （emmer 到硬粒小麦） 驯化中对氮可用性的不同基因表达反应。值得注意的是，氮触发的硬粒小麦基因表达是 emmer 和野生 emmer 的两倍。在每个阶段都确定了独特的选择特征：初级驯化主要影响与生物相互作用相关的基因，而次级驯化影响与氨基酸代谢相关的基因，特别是赖氨酸。在差异表达基因 （DEGs） 中发现选择特征，特别是那些与氮代谢相关的基因，例如编码谷氨酸脱氢酶 （GDH） 的基因。总体而言，我们的研究强调了氮的可用性在主要粮食作物的驯化和适应性反应中的关键作用，在不同性状和生长条件下具有不同的影响。