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

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العنوان: HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications.
المؤلفون: Mansueto L; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Tandayu E; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Mieog J; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Garcia-de Heer L; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Das R; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Burn A; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia., Mauleon R; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia.; International Rice Research Institute, Pili Drive, Los Banos, Laguna, Philippines., Kretzschmar T; Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia. Tobias.Kretzschmar@scu.edu.au.
المصدر: BMC genomics [BMC Genomics] 2024 Aug 29; Vol. 25 (1), pp. 818. Date of Electronic Publication: 2024 Aug 29.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Polymorphism, Single Nucleotide* , Cannabis*/genetics , Genotyping Techniques*/methods , Medical Marijuana*, High-Throughput Nucleotide Sequencing/methods ; Genome, Plant ; Genotype
مستخلص: 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.
(© 2024. The Author(s).)
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معلومات مُعتمدة: PhD stipend Southern Cross University; LP210200606 Australian Research Council
فهرسة مساهمة: Keywords: Cannabis sativa; Genetic fingerprints; Genotyping; Integer linear programming; Plant breeding; Quantitative trait loci; SNP
المشرفين على المادة: 0 (Medical Marijuana)
تواريخ الأحداث: Date Created: 20240829 Date Completed: 20240830 Latest Revision: 20240902
رمز التحديث: 20240902
مُعرف محوري في PubMed: PMC11363669
DOI: 10.1186/s12864-024-10734-z
PMID: 39210290
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-024-10734-z