The Coix genome provides insights into Panicoideae evolution and papery hull domestication

Abstract Coix is a grass crop domesticated as early as 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 lack of a sequenced genome. Here we report de novo sequencing and assembly of the 1,619 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 rather than maize, but intriguingly only Coix and maize had a recent whole 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 one (thick, hard-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 resulted from 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.