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Abstract Detail

Population Genetics/Genomics

McCormick, Anna Halpin [1], Law, Kerin [2], Heyduk, Karolina [3], Kantar, Michael [1], Masalia, Rishi [2].

Insights from publicly available sequence data for Cannabis sativa.

The human association with Cannabis  dates back over 24,000 years ago, with domestication likely to have occurred at multiple independent locations across Eurasia during the Holocene. These domesticated populations served the community through the provision of fiber and medicine and likely accelerated a division in the genus with varietals broadly known today as fiber-type (hemp) and drug-type (marijuana).  With prohibition ending across much of the world the increasing accessibility and affordability of high throughput sequencing has seen a number of groups creating publicly available Cannabis genomic datasets in the interest of furthering research. Across these public datasets, a wide array of Cannabis varietals are represented (hemp, drug and medicinal). Here we aim to provide a comprehensive survey of these publicly available populations. Data from eight different public projects were downloaded as raw sequence (fastq) and aligned to the CBDRx reference genome using BWA-mem. SNPs were called using bcftools and filtered using vcftools with a minor allele frequency of 0.05, Hardy-Weinberg equilibrium of 0.05, mapping quality of 30 and max missingness of 10%. Using chloroplast, mitochondria and nuclear data, different levels of diversity and admixture were observed within and between publicly available collections and across different chromosomal regions. Using this approach, we stratified cultivars by use type and examined the impact domestication has had across the different groups of germplasm.  Understanding the genetic structure and levels of admixture of cannabis at the population level is important for the definitions and identification of rare and elite cultivars. We hope that our analysis will aid breeding strategies through the examination of the genetic landscape across chromosomes and surrounding genes of agronomic importance to facilitate crop improvement.

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1 - University Of Hawaii, Tropical Plant And Soil Sceinces, St. John Plant Science Lab, Room 102, 3190 Maile Way , Honolulu, HI, 96822, United States
2 - LeafWorks Inc, 130 South High Street, Sebastopol, CA, 95472, USA
3 - University Of Hawai'i, School Of Life Sciences, 1800 East-West Road, Honolulu, HI, 96822, United States

Public Data
Genome skimming.

Presentation Type: Oral Paper
Session: PGG3, Population Genetics and Genomics III
Location: /
Date: Wednesday, July 21st, 2021
Time: 1:30 PM(EDT)
Number: PGG3005
Abstract ID:504
Candidate for Awards:Margaret Menzel Award

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