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

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

作者机构：Southern Cross Univ Fac Sci & Engn Southern Cross Plant Sci 1 Mil Rd East Lismore NSW 2480 Australia Int Rice Res Inst Pili Dr Laguna Philippines 

出 版 物：《BMC GENOMICS》 (BMC基因)

年 卷 期：2024年第25卷第1期

页      面：1页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 0836[工学-生物工程] 

基　　金：Southern Cross University [LP210200606] Australian Research Council (ARC) [LP210200606] Australian BioCommons Leadership Share (ABLeS) pro-gram - Bioplatforms Australia Australian Research Council [LP210200606] Funding Source: Australian Research Council 

主　　题：Cannabis sativa Genotyping SNP Plant breeding Quantitative trait loci Integer linear programming Genetic fingerprints 

摘      要：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 chrom