Lovell John T, Schwartz Scott, Lowry David B, Shakirov Eugene V, Bonnette Jason E, Weng Xiaoyu, Wang Mei, Johnson Jenifer, Sreedasyam Avinash, Plott Christopher, Jenkins Jerry, Schmutz Jeremy, Juenger Thomas E
Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA;
Genome Res. 2016 Apr;26(4):510-8. doi: 10.1101/gr.198135.115. Epub 2016 Mar 7.
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
气候适应是适合度的基因型与环境相互作用（G×E）的一个例子。对基因表达调控变异的选择可促成适应性表型多样性；然而，令人惊讶的是，很少有研究考察全基因组基因表达G×E模式如何在响应环境胁迫和其他导致气候适应的选择因子时得以体现。在此，我们描述了多年生C4禾本科植物哈利大黍（Panicum hallii）的高地（适应干旱）和低地（中生）生态型在自然田间条件下对干旱响应的表达差异。总体而言，我们发现顺式调控元件促成了47%的基因的表达差异，其中7.2%表现出对干旱响应的G×E。虽然所占比例较小，但我们观察到1294个基因（7.8%）具有反式效应。反式与环境的相互作用比顺式G×E更弱且更不常见，仅在0.7%的反式调控基因中出现。最后，基因表达杂种优势在具有显著G×E的表达表型中高度富集。因此，驱动杂种优势的遗传模式，如显性或超显性，在G×E基因中可能很常见。有趣的是，干旱响应转录因子特有的基序在表现出G×E和反式调控的基因启动子中高度富集，表明表达G×E和杂种优势可能源于转录因子或其结合位点的进化。哈利大黍是其近缘种且新兴的生物燃料作物柳枝稷（Panicum virgatum）的基因组模型。因此，这里的结果不仅有助于发现本地适应背后的遗传机制，还为在水分受限条件下提高柳枝稷产量提供了基础。
