Coix is a grass crop domesticated as early as the Neolithic era. It is still widely cultivated for both highly nutritional food and medicinal use. However, the genetic study and breeding of this crop are hindered by the lack of a sequenced genome. Here, we report de novo sequencing and assembly of the 1619-Mb genome of Coix, and annotation of 75.39% repeats and 39 629 protein-coding genes. Comparative genomics analysis showed that Coix is more closely related to sorghum than maize, but intriguingly only Coix and maize had a recent genome duplication event, which was not detected in sorghum. We further constructed a genetic map and mapped several important traits, especially the strength of hull. Selection of papery hull (thin: easy dehulling) from the stony hull (thick: difficult dehulling) in wild progenitors was a key step in Coix domestication. The papery hull makes seed easier to process and germinate. Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis. We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci (QTLs), which are associated with hull thickness and color, respectively. The two QTLs were further fine mapped within intervals of 250 kb and 146 kb, respectively. These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

ix是一种早在新石器时代就已驯化的草类作物。它仍然被广泛种植用于高营养食品和医药用途。但是，由于缺少基因组测序，阻碍了该作物的遗传研究和育种。在这里，我们报道了Coix的1619-Mb基因组从头测序和装配，并注释了75.39％的重复序列和39629个蛋白质编码基因。比较基因组学分析表明，Coix与高粱的关系比玉米更紧密，但有趣的是只有Coix玉米最近发生了基因组复制事件，高粱中未检测到。我们进一步构建了遗传图谱，并绘制了一些重要特征，尤其是船体的强度。在野生ix中从石质船体（薄：难脱壳）中选择纸质船体（薄：易脱壳）是Coix的关键步骤驯化。纸质外壳使种子更易于加工和发芽。解剖和整体转录组分析表明，纸质船体是抑制细胞分裂和壁生物发生的结果。我们还成功地证明了种子壳耐压性受两个主要的数量性状基因座（QTL）控制，它们分别与壳的厚度和颜色有关。分别在250 kb和146 kb的间隔内进一步精细映射了两个QTL。这些资源为进化研究提供了平台，并将促进这一重要作物的分子育种。