The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.

序列变异对植物适应性的影响程度尚不清楚。由于非编码序列的功能注释仍然稀疏，详细描述作用于基因组的约束（尤其是在调控位点）的高分辨率图谱将是有益的。在这里，我们提出了水稻（ Oryza sativa ）的适应度结果（fitCons）图。我们推断了源自九个功能基因组和表观基因组数据集的 246 个推断基因组类别的 fitCons 分数 ( ρ )，包括染色质可及性、信使 RNA/小 RNA 转录、DNA 甲基化、组蛋白修饰和参与的 RNA 聚合酶活性。这些数据与来自 1,477 个水稻品种和 11 个稻科参考基因组序列的全基因组多态性和分歧数据进行了整合。我们发现ρ是多峰的，大约9% 的水稻基因组属于其中一半以上的碱基如果突变可能会产生适应性结果的类别。大约 2% 的水稻基因组显示出弱负选择的证据，通常出现在候选调控位点，包括一组 1,000 个潜在活性增强子元件。该 fitCons 图提供了与基因组多样性相关的进化力量的视角，有助于基因组注释，并可以指导作物育种计划。