Gene copy number is associated with phytochemistry in Cannabis sativa.

Daniela Vergara,Nolan C Kane,Reggie Gaudino,Ezra L Huscher,Robert M Givens,Kyle G Keepers,Christian G Cizek,Anthony Torres,Heidrun Huber

doi:10.1093/aobpla/plz074

Daniela Vergara, Nolan C Kane + Show 7 more

Open Access

https://doi.org/10.1093/aobpla/plz074

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Abstract

Gene copy number (CN) variation is known to be important in nearly every species where it has been examined. Alterations in gene CN may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids—THCA (delta-9-tetrahydrocannabinolic acid) and CBDA (cannabidiolic acid)—are products of a three-step biochemical pathway. Using whole-genome shotgun sequence data for 69 Cannabis cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in CN. Transcriptome sequence data show that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that CN partially explains variation in cannabinoid content levels among Cannabis plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped CN variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.

Highlights

Gene copy number (CN) varies among individuals of the same species, which may have considerable phenotypic impacts (Stranger et al 2007; Gaines et al 2010)
We found a cluster of four genes, three from the Pineapple Banana Bubba Kush (PBBK) assembly and one from the Purple Kush (PK) assembly, that we infer to be cannabichromenic acid (CBCA) synthases
CN variation in some genes involved in cannabinoid production has been previously reported, here we estimate CN variation in multiple steps of the biochemical pathway in 67 Cannabis genomes from multiple varieties within the broad-leaf, narrowleaf and hemp groupings (Lynch et al 2016) using two genome assemblies constructed via complementary technologies

Summary

Introduction

Gene copy number (CN) varies among individuals of the same species, which may have considerable phenotypic impacts (Stranger et al 2007; Gaines et al 2010). Both genome size and complexity can be increased by gene duplication (Losos et al 2013), and new genes can be adaptive (Losos et al 2013). CN variation can provide a path to rapid evolution in strong selective regimes (Gaines et al 2010), such as changing environments (Żmieńko et al 2014; Hardigan et al 2016) or domestication (Swanson-Wagner et al 2010; Ollivier et al 2016).

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