HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications

Locedie Mansueto; Erwin Tandayu; Jos Mieog; Lennard Garcia-de Heer; Rekhamani Das; Adam Burn; Ramil Mauleon; Tobias Kretzschmar

doi:10.1186/s12864-024-10734-z

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HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications

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HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications

Locedie Mansueto, Erwin Tandayu, Jos Mieog, Lennard Garcia-de Heer, Rekhamani Das, Adam Burn, Ramil Mauleon and Tobias Kretzschmar

BMC genomics, Vol.25(1), 818

29/08/2024

DOI: https://doi.org/10.1186/s12864-024-10734-z

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Abstract

Cannabis sativa

Genotyping

SNP

Plant breeding

Quantitative trait loci

Integer linear programming

Genetic fingerprints

Background Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. Results The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. Conclusion HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.

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Title: HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications
Creators: Locedie Mansueto - Southern Cross University, Faculty of Science and Engineering
Erwin Tandayu - Southern Cross University
Jos Mieog - Southern Cross University
Lennard Garcia-de Heer - Southern Cross University
Rekhamani Das - Southern Cross University
Adam Burn - Southern Cross University
Ramil Mauleon - International Rice Research Institute
Tobias Kretzschmar - Southern Cross University
Publication Details: BMC genomics, Vol.25(1), 818
Publisher: BioMed Central Ltd.
Grants: New crop on the block: The genetic control of hempseed nutritional quality, LP210200606, Australian Research Council (Australia, Canberra) - ARC
Grant note: This study was funded by the Australian Research Council (ARC) Linkage project LP210200606.
Identifiers: 991013219802702368
Academic Unit: Faculty of Science and Engineering; Science
Language: English
Resource Type: Journal article

HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications

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