Data from: The role of cis regulatory evolution in maize domestication

Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ~17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ~70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

由顺式调控元件（cis regulatory element）修饰所导致的不同进化支间的基因表达差异，被认为在演化进程中发挥重要作用。本研究针对玉米（maize）及其野生祖先大刍草（teosinte）的全基因组范围顺式调控元件与反式调控元件（trans regulatory element）差异展开分析，以三种组织类型（雌穗、叶片与茎秆）的F1杂交系及亲本自交系为材料，采用深度RNA测序技术进行检测。
研究观测到广泛存在的调控变异：在约17000个基因中，近70%的基因表现出玉米与大刍草间存在调控分化的证据。然而，在所有已采样的玉米与大刍草品系中，表现出稳定顺式调控差异的基因仅为1079个，数量远少于前者。在这1079个基因中，约70%的顺式调控差异仅存在于单一组织中。
顺式调控差异基因数量最多的组织为雌穗组织——该组织在驯化过程中经历了剧烈的形态重塑。正如驯化瓶颈效应所预期的那样，玉米的顺式调控变异丰度低于大刍草，且在表现出玉米-大刍草顺式调控分化的基因中，这一丰度差异最为显著，这表明驯化过程中对顺式调控差异存在选择作用。与顺式调控元件受选择的预期一致，携带顺式调控效应的基因与玉米驯化及改良过程中受正向选择的基因呈现显著相关性，而携带反式调控效应的基因则无此关联。
研究还观测到一种方向偏好性：携带顺式调控差异的基因中，玉米等位基因的表达水平高于大刍草等位基因的情况更为常见，这表明驯化过程倾向于促进基因表达的上调。最后，本研究系统记录了三种组织中超过17000个基因的玉米与大刍草间顺式及反式调控变化。