Research record6 February 2025Journal article
Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild-growing and cultivated cannabis
Manica Balant, Daniel Vitales, Zhiqiang Wang, Zoltán Barina, Lin Fu, Tiangang Gao, Teresa Garnatje, Airy Gras, Muhammad Q. Hayat, Marine Oganesian, Jaume Pellicer, Alireza S. Salami, Alexey P. Seregin, Nina Stepanyan-Gandilyan, Nusrat Sultana, Shagdar Tsooj, Magsar Urgamal, Joan Vallès, Robin van Velzen, Lisa Pokorny
Plants, People, Planet · 2025
Abstract
(EN) Cannabis has been used by humans for millennia, resulting in diverse landraces and uses. Its complex legal status and economic importance make sampling wild‐growing populations difficult, limiting past studies to modern cultivars with low genetic diversity. Our research provides crucial insights into the genetic diversity of wild‐growing and cultivated cannabis. We identified three major genetic groups—E Asia, Paleotropis, and Boreal—shedding light on evolutionary relationships within the genus. Understanding cannabis genetic structure supports conservation, sustainable breeding, and informed policy decisions. These findings lay a foundation for future research, ensuring the responsible use and preservation of this economically significant plant. Cannabis has provided important and versatile services to humans for millennia. Domestication and subsequent dispersal have resulted in various landraces and cultivars. Unravelling the phylogeography of this genus poses considerable challenges because of its complex history. We relied on a Hyb‐Seq approach (combining target capture with shotgun sequencing), with the universal Angiosperms353 enrichment panel, to explore the genetic structure of wild‐growing cannabis accessions and cultivars by implementing phylogenomic and population genomic workflows on the same Hyb‐Seq data. Our findings support the treatment of Cannabis as a monotypic genus (C. sativa L.), structured into three main genetic groups—E Asia, Paleotropis, and Boreal—with clear phylogeographic signal despite significant levels of admixture. The E Asia group was sister to the Paleotropis and the Boreal groups. Individuals within the Paleotropis group could be further structured into three subgroups: Iranian Plateau, C & S China and Himalayas, and Indoafrica. Individuals from the Boreal group split into two subgroups: Eurosiberia and W Mongolia and Caucasus and Mediterranean. Hemp and drug‐type landraces and cultivars consistently matched their putative geographic origin. These findings enhance our understanding of the genetic patterns in cannabis and provide a framework for future research into its current and past genetic diversity.
The paper's abstract, reproduced as published.
Record created 4 May 2026 · maintained by landrace.wiki editors ·
page history
Published6 Feb 2025
TypeJournal article
VenuePlants, People, Planet
Year2025
2025-02-06
2026-05-04
Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild-growing and cultivated cannabis
Journal article
Genetics
Manica Balant, Daniel Vitales, Zhiqiang Wang, Zoltán Barina, Lin Fu, Tiangang Gao, Teresa Garnatje, Airy Gras, Muhammad Q. Hayat, Marine Oganesian, Jaume Pellicer, Alireza S. Salami, Alexey P. Seregin, Nina Stepanyan-Gandilyan, Nusrat Sultana, Shagdar Tsooj, Magsar Urgamal, Joan Vallès, Robin van Velzen, Lisa Pokorny
Plants, People, Planet
2025
10.1002/ppp3.70043
https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.70043
https://nph.onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.70043
Global phylogeographic study using a Hyb-Seq approach that combines target capture (with the universal Angiosperms353 enrichment panel) and shotgun whole-genome sequencing on the same data, applied to wild-growing accessions, cultivars and herbarium specimens drawn from natural history collections. Phylogenomic and population genomic workflows on the integrated dataset support treating Cannabis as a monotypic genus and recover three main genetic groups: East Asia, Paleotropis, and Boreal. Paleotropis is further divided into Iranian Plateau, Central and South China–Himalayas, and Indoafrica subgroups. Boreal is divided into Eurosiberia–West Mongolia and Caucasus–Mediterranean subgroups. The strongest signal in the data is geographic rather than use-type, with cultivars clustering by region of origin rather than by hemp/drug distinction. Iranian and Central Asian wild-growing populations emerge as particularly distinctive and morphogenetically diverse, consistent with the idea that this region functions as a genetic melting pot. The study is the first global landrace-inclusive phylogeography of cannabis after Ren et al. 2021 and is methodologically significant for showing that herbarium specimens (including older natural history collections) can be integrated with fresh material to recover phylogenetic signal in a genus where field sampling is legally difficult. Provides the geographic backbone against which any landrace genotype on the wiki can be situated, complements the Lynch et al. 2025 pangenome at the population scale, and supports the conservation case that wild-growing populations from understudied regions hold diversity not represented in modern cultivars.
(EN) Cannabis has been used by humans for millennia, resulting in diverse landraces and uses. Its complex legal status and economic importance make sampling wild‐growing populations difficult, limiting past studies to modern cultivars with low genetic diversity. Our research provides crucial insights into the genetic diversity of wild‐growing and cultivated cannabis. We identified three major genetic groups—E Asia, Paleotropis, and Boreal—shedding light on evolutionary relationships within the genus. Understanding cannabis genetic structure supports conservation, sustainable breeding, and informed policy decisions. These findings lay a foundation for future research, ensuring the responsible use and preservation of this economically significant plant. Cannabis has provided important and versatile services to humans for millennia. Domestication and subsequent dispersal have resulted in various landraces and cultivars. Unravelling the phylogeography of this genus poses considerable challenges because of its complex history. We relied on a Hyb‐Seq approach (combining target capture with shotgun sequencing), with the universal Angiosperms353 enrichment panel, to explore the genetic structure of wild‐growing cannabis accessions and cultivars by implementing phylogenomic and population genomic workflows on the same Hyb‐Seq data. Our findings support the treatment of Cannabis as a monotypic genus (C. sativa L.), structured into three main genetic groups—E Asia, Paleotropis, and Boreal—with clear phylogeographic signal despite significant levels of admixture. The E Asia group was sister to the Paleotropis and the Boreal groups. Individuals within the Paleotropis group could be further structured into three subgroups: Iranian Plateau, C & S China and Himalayas, and Indoafrica. Individuals from the Boreal group split into two subgroups: Eurosiberia and W Mongolia and Caucasus and Mediterranean. Hemp and drug‐type landraces and cultivars consistently matched their putative geographic origin. These findings enhance our understanding of the genetic patterns in cannabis and provide a framework for future research into its current and past genetic diversity.
