Talk:Quantitative trait locus

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Discussion for: Quantitative trait locus • View • Links • Related changes

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Page scope

Quantitative trait locus covers what a quantitative trait locus is, the populations and methods used to map one, what the reported figures measure, and what has been mapped in cannabis, by population. The inheritance of chemotype, sex and day-length insensitivity as traits belongs to Genetic traits, the genetic share of variance to Heritability, and the interaction between genotype and environment to Genotype-by-environment interaction.

Data verification

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

Discussion

Sources

Lübberstedt, Beavis and Suza (2023), "Cluster Analysis, Association, and QTL Mapping", chapter 5 of Molecular Plant Breeding: population types, single-marker analysis, interval, composite interval and multiple interval mapping, linkage disequilibrium, association mapping, structure and multiple testing.
Beavis, Mahama and Suza (2023), "Linkage", chapter 2 of Quantitative Genetics for Plant Breeding: Sax and the 60 years that followed.
Lander and Botstein (1989), Genetics 121: 185–199; Zeng (1994), Genetics 136: 1457–1468; Xu (2003), Genetics 165: 2259–2268; Bernardo (2008), Crop Science 48: 1649–1664: interval mapping, composite interval mapping, the Beavis effect and how little of what was mapped reached breeding.
Malosetti, Ribaut and van Eeuwijk (2013), Frontiers in Physiology 4: 44: QTL-by-environment models.
Weiblen and colleagues (2015), New Phytologist 208: 1241–1250, and Grassa and colleagues (2021), New Phytologist 230: 1665–1679: Skunk No. 1 × Carmen.
Laverty and colleagues (2019), Genome Research 29: 146–156: Purple Kush × Finola.
Woods and colleagues (2021), Genetics 219: iyab099: Carmagnola × USO31.
Manansala-Siazon and colleagues (2025), Plants 14: 3853: IPK_CAN_57 × SI-1.
Faux and colleagues (2016), Euphytica 209: 357–376; Stack and colleagues (2024), Molecular Plant-Microbe Interactions 37: 51–61; Toth and colleagues (2022), Frontiers in Plant Science 13: 991680; Dowling and colleagues (2024), The Plant Journal 119: 383–403; Tang and colleagues (2026), Scientific Reports 16: 32880; Zhao and colleagues (2022), BMC Plant Biology 22: 250; Seifi and colleagues (2025), Frontiers in Plant Science 16: 1543229: single crosses and pooled scans.
Stack and colleagues (2025), International Journal of Molecular Sciences 26: 1165: recombination rates and the realignment of the Early1 data.
Petit and colleagues (2020), Frontiers in Plant Science 11: 569958, and Frontiers in Genetics 11: 566314: the panel of 123 hemp accessions.
de Ronne and colleagues (2024), Scientific Reports 14: 9162, and de Ronne and Torkamaneh (2025), The Plant Genome 18: e70031: the Canadian drug-type panel.
Welling and colleagues (2020), Scientific Reports 10: 18643: pools from the Ecofibre collection.
Babaei and Torkamaneh (2026), The Plant Genome 19: e70243: the Iranian landrace panel.

Where the sources disagree

A locus for total cannabinoid content in Skunk No. 1 × Carmen. Weiblen and colleagues (2015) call it putative: LOD 3.30 on linkage group 1, above the group-wise threshold of 2.18 and below the experiment-wise threshold of 3.42. Laverty and colleagues (2019) describe the same study as identifying a locus "displaying a strong association" with total content, about 1.2 cM from marker ANUCS501.
Seed size and plant size. In Woods and colleagues seed mass was correlated with plant height and stem diameter and most of its QTLs overlapped agronomic clusters. In Manansala-Siazon and colleagues seed traits and plant traits were not correlated. The second paper also points to a difference of design: Woods's seed came from open pollination among segregating F2 plants, and theirs from one pollen source applied to all plants.
"Single QTL" in Woods and colleagues. The discussion says single QTLs were identified for seed yield, thousand-seed mass and dry biomass. Table 1 of the same paper gives five, four and four. The sentence reads most easily as saying that these traits have a QTL outside the four clusters.
Fibre-quality QTLs across three sites. The abstract of Petit and colleagues (2020) in Frontiers in Genetics says six were found across the three environments. The results section gives eight across three and eight across two.
Alleles of the chromosome 9 height QTL in Manansala-Siazon and colleagues. The results give GG as tall (121 cm) and AA as short (66 cm). The discussion says AA homozygotes were nearly twice as tall. The results also give the LOD of the seed-weight QTL as 14.15, and the discussion as 14.5.
The term "accession" in Babaei and Torkamaneh. The paper speaks of 145 accessions, 72 female and 73 male. The methods describe these as pooled samples, of plants of one sex within each block, from 25 populations. The cannabinoid methods describe sampling from female plants.
Earlier hemp QTLs. Tang and colleagues (2026) write that genomic regions governing flowering time in industrial hemp had not been reported. Petit and colleagues (2020), Toth and colleagues (2022) and Dowling and colleagues (2024) report such regions.

How far the evidence goes

The variance percentages are those the authors report for the samples they mapped. Population sizes run from 62 plants to 706, which matters for the size of the estimates by the reasoning of Beavis and Xu.
Most results come from one site in one season. Carmagnola × USO31 was one field in 2017. The Iranian panel was one greenhouse complex. Only the 123-accession panel in the article compares sites, in one season, 2013.
A cross samples the two parent plants. IPK_CAN_57 × SI-1 began from one plant of each accession, so its QTLs are differences between those two plants and do not describe the landrace accession as a population.
The Iranian panel covers Iranian populations. No cited study maps landrace populations from another region as a panel. The 123-accession panel lists landraces among its mainly fibre accessions and gives no separate result for them.
The authors of the Iranian panel take its main loci to be fixed in modern cultivars and polymorphic in landraces. That reading rests on the comparison with the Canadian drug-type panel, grown separately and with a different mix of chemotypes.
Candidate genes differ in their standing. Olivetol synthase was tested in yeast and the LOC115716363 gene in rice. TINY is an untested hypothesis, and Manansala-Siazon and colleagues call their own candidates highly speculative.
The Skunk No. 1 × Carmen figures of 2015 and 2021 use different plant numbers and marker sets, and the group numbers differ: the ratio QTL is on linkage group 6 in 2015 and chromosome 7 in 2021.

Terms

QTL: quantitative trait locus. Some panel papers use it for a single significant marker and others for a cluster of collinear markers.
LOD: logarithm of the odds. PVE: phenotypic variance explained.
Bulk segregant analysis, BSA, BSA-seq, QTL-seq and XP-GWAS all compare pools of plants from the two extremes of a trait. BSR-seq does so with RNA sequencing.
Numbering of chromosomes. Purple Kush and Finola assemblies and CBDRx (cs10) number some chromosomes differently. Woods and colleagues follow Laverty's numbering; Grassa, de Ronne and Babaei use CBDRx.

Further figures from the sources

Carmagnola × USO31, share of variance of the largest QTL for each trait in per cent: plant height 22.35, seed yield 12.92, thousand-seed mass 18.16, stem diameter 20.13, dry biomass 24.19, THCA 32.10, CBGA 35.21, β-caryophyllene 43.88, geraniol 43.33.
IPK_CAN_57 × SI-1: hundred-seed weight 26.59, seed volume 33.24, seed width 31.46, seed length 34.44, longest branch 39.20, stem diameter 38.12. The map is 291.5 cM from 455 SNPs. The Skunk No. 1 × Carmen map of 2021 is 818.6 cM from 1,235 markers.
Canadian drug-type panel: CBC 89.1 at one marker on chromosome 7, CBD 66.0 at the same marker, CBN 53.4, CBG 56.7.
Iranian landrace panel: THCA 91.4, CBN 89.9 and Δ9-THC 72.9 at the chromosome 5 marker; CBGA 90.6; number of nodes on the main inflorescence 87.1; flowering at 50 per cent 30.6.