A high-throughput segregation analysis identifies the sex chromosomes of Cannabis sativa

Cannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. The C. sativa sex chromosomes sequence would allow early sexing and better management of this crop; however, the C. sativa genome projects failed to identify the sex chromosomes so far. Moreover, dioecy (separate sexes) in the Cannabaceae family is expected to be ancestral, not clear whether the chromosomes, which are homomorphic, are of recent or more ancient origin. Here we RNA-sequenced a C. sativa family (2 parents and 10 male and female offspring) and performed a segregation analysis for all C. sativa genes using a probabilistic method, SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified a single chromosome pair. Further analysis of the >500 sex-linked genes revealed that C. sativa has a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far.