Talk:Genetic marker

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Discussion for: Genetic marker • View • Links • Related changes

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Page scope

Genetic marker covers what a genetic marker is, the main kinds of marker, what a set of markers can claim, and the markers used in cannabis studies for sex, chemotype, population structure and identity. The sex system and the published accuracy of sexing assays belong to Sex determination in cannabis, the inheritance of chemotype to Genetic traits, mapping to Quantitative trait locus, the measures and figures of diversity to Genetic diversity and Heterozygosity, and ancestry assignment to Introgression and Gene flow.

Data verification

Record source conflicts, figures that differ between studies and sources not used here. Keep narrative content on the article.

Discussion

Sources

Lübberstedt, Bhattacharyya and Suza (2023), "Markers and Sequencing", and Lübberstedt, Beavis and Suza (2023), "Marker Assisted Selection and Genomic Selection", in Molecular Plant Breeding: what a marker is, the wanted properties, tagging and fingerprinting, DNA and non-DNA markers, transfer between populations.
Williams and colleagues (1990), Vos and colleagues (1995) and Tautz (1989), Nucleic Acids Research, and Elshire and colleagues (2011), PLoS ONE 6: e19379: the RAPD, AFLP, microsatellite and genotyping-by-sequencing methods as first described.
Jones and colleagues (1997), Molecular Breeding 3: 381–390: reproducibility of RAPD, AFLP and SSR between laboratories.
Nybom (2004), Molecular Ecology 13: 1143–1155: 307 studies of wild plants. Väli and colleagues (2008), Molecular Ecology 17: 3808–3817: carnivores. Putman and Carbone (2014), Ecology and Evolution 4: 4399–4428: microsatellite data. Lachance and Tishkoff (2013), BioEssays 35: 780–786: human genotyping arrays.
Ouborg and colleagues (2010), Trends in Genetics 26: 177–187, and Bernardo (2008), Crop Science 48: 1649–1664: neutral markers in conservation and markers in plant breeding.
Mandolino and Carboni (2004), Euphytica 140: 107–120, and Welling and colleagues (2016), Frontiers in Plant Science 7: 1113: reviews of markers in hemp and of Cannabis genetic resources.
Sakamoto and colleagues (1995, 2005), Mandolino and colleagues (1999), Törjék and colleagues (2002), Techen and colleagues (2010), Toth and colleagues (2020), Prentout and colleagues (2025), Riera-Begué and colleagues (2025): sex markers.
de Meijer and colleagues (2003), Kojoma and colleagues (2006), Staginnus and colleagues (2014), Wenger and colleagues (2020), Toth and colleagues (2020), Allen and colleagues (2026): chemotype markers.
de Meijer and Keizer (1996), Faeti and colleagues (1996), Forapani and colleagues (2001), Hillig (2005), Gilmore and colleagues (2003, 2007), Datwyler and Weiblen (2006), Sawler and colleagues (2015), Lynch and colleagues (2016), Dufresnes and colleagues (2017), Soorni and colleagues (2017), Zhang and colleagues (2018), Henry and colleagues (2020), Babaei and Torkamaneh (2026): surveys of accessions and populations.
Gillan and colleagues (1995), Alghanim and Almirall (2003), Howard and colleagues (2008), Mendoza and colleagues (2009), Köhnemann and colleagues (2012), Soler and colleagues (2017), Schwabe and McGlaughlin (2019), Cull and Joly (2025): identity of plants and cultivars.
Somody and Molnár (2025), Plants 14: 594: yellow stem in hemp.

Where the sources disagree

Fixed differences between hemp and drug type. Datwyler and Weiblen (2006) report 18 AFLP bands fixed between three fibre populations and one drug cultivar and call them useful for discriminating cultivars. Sawler and colleagues (2015) found no SNP fixed between 43 hemp and 81 drug-type samples. The designs and marker systems differ, and the first compares a single drug cultivar.
Telling hemp from drug type. Gilmore and colleagues (2003) could not assign plants unequivocally with five loci. Dufresnes and colleagues (2017) assigned plants correctly with 13 loci and a reference set of 1,324 plants, while their conservative test left many plants unassigned.
Geographic origin. Gilmore and colleagues (2003) and Datwyler and Weiblen (2006) name the geographic source of seizures as a possible use of their markers. Mendoza and colleagues (2009) report that six loci did not relate samples from the same state.
Species. Hillig (2005) proposes three species from allozyme frequencies. Welling and colleagues (2016) call further taxonomic divisions controversial, on the grounds that the plants readily intercross and that no validated natural populations are reported.
The size of a band in Riera-Begué and colleagues (2025). The text gives the digested Y amplicon as 157 and 262 base pairs, which sum to the 419 of the uncut amplicon. Panel b of Figure 1 labels the longer piece 267.
Törjék and colleagues (2002). The title names the markers MADC5 and MADC6; the abstract of the same paper names them MADC3 and MADC4.
Forapani and colleagues (2001). Heterozygosity per variety runs from 0.05 to 0.26, and the average over all loci and plants is given as 0.29.

How far the evidence goes

The sex assays in the laboratory: Prentout and colleagues on 12 hemp cultivars with 1 to 33 samples each, Riera-Begué and colleagues on 14 hemp-type cultivars and six crosses. Drug-type material in both is in silico, from published genomes.
The chemotype test across kinds of plant: Wenger and colleagues on feral plants from one Minnesota river valley, clinical cultivars and grain cultivars. Whether sex and chemotype assays hold in landrace populations is not settled by these tests.
Väli and colleagues measured carnivores and Lachance and Tishkoff human arrays. They illustrate how such biases work. Neither measures the size of the effect in Cannabis.
Yellow stem appears in Somody and Molnár (2025) as a trait selected in breeding. It is visible and follows one gene; that paper does not use it to map other genes.
Babaei and Torkamaneh's statement that their main loci are fixed in modern cultivars draws on a separate drug-type panel (de Ronne and Torkamaneh 2025).
Cull and Joly's six SNPs separated the cultivars in silico. Their panel of 20 was tested on the sequenced plants and on nine dried-flower samples of three cultivars.
Lynch and colleagues' caution about "landrace genetics" concerns plants from producers, breeders and seed sellers. It does not describe landraces collected in the field.

Terms

SSR and STR: simple sequence repeat and short tandem repeat, other names for a microsatellite. The forensic papers say STR.
SCAR: sequence-characterised amplified region, a band converted into a marker with primers specific to its sequence.
Dominant and codominant, of a marker: whether a heterozygote can be told from a homozygote.
Fixed: one allele present in all plants of a group.
In silico: tested by computer against published sequences, with no laboratory assay.