An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
- Djivan Prentout1,
- Olga Razumova2,3,
- Bénédicte Rhoné1,4,
- Hélène Badouin1,
- Hélène Henri1,
- Cong Feng5,6,
- Jos Käfer1,
- Gennady Karlov2 and
- Gabriel A.B. Marais1
- 1Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université Lyon 1, CNRS, F-69622 Villeurbanne, France;
- 2Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia;
- 3N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow 127276, Russia;
- 4Institut de Recherche pour le Développement, UMR DIADE, IRD, Université de Montpellier, F-34394 Montpellier, France;
- 5Chongqing Medical University, Yuzhong District, Chongqing, 400016, China;
- 6BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
Abstract
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. Identifying the sex chromosome sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects have failed to do so. Moreover, as dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study, as little is known about old plant sex chromosomes. Here, we RNA-sequenced a C. sativa family (two parents and 10 male and female offspring, 576 million reads) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified the largest chromosome pair being the sex chromosomes. We found that the X-specific region (not recombining between X and Y) is large compared to other plant systems. Further analysis of the sex-linked genes revealed that C. sativa has a strongly degenerated Y Chromosome and may represent the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large, highly divergent nonrecombining regions, yet still be roughly homomorphic.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.251207.119.
- Received July 31, 2019.
- Accepted January 24, 2020.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
