Genetic traits
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Genetic traits are characters of an organism that differ among individuals and are passed from parents to offspring. In Cannabis a few of them segregate in crosses as if a single gene controlled each one: the sex of a plant, its chemotype (whether it makes mainly tetrahydrocannabinol (THC), mainly cannabidiol (CBD) or both) and, in some lines, flowering regardless of day length. Others, among them flowering time, height, yield and the total amount of cannabinoids a plant produces, vary continuously, are influenced by several or many loci and change with the conditions in which the plant grows.[1][2][3]
The enzymes that make the acid forms of THC and CBD are coded at separate loci. Their tight linkage is why chemotype is inherited as though one gene were responsible.[4][5] The sex chromosomes set a plant's chromosomal sex, while the share of male and female flowers on it is a quantitative character of its own.[6] Traits also differ in how far their variation is inherited. In trials of hemp and of drug-type cannabis, flowering dates were largely genetic and the ratios between cannabinoids stayed stable, while height, stem weight and the absolute quantities of cannabinoids moved with the environment.[7][8]
Discrete and continuous traits
Some traits fall into separate classes and others vary along a continuous scale. In 1918 the statistician Ronald Fisher proposed a model that reconciled the inheritance of the two kinds in breeding populations. The model plant breeders use for a measured trait divides the phenotypic value of a plant into its genotypic value and a non-genetic part, mostly the effect of the environment.[9]
The share of the variation among plants that is genetic is the trait's heritability. Heritability in the broad sense counts all the genetic variance. Heritability in the narrow sense counts only its additive part, the extent to which phenotypes are set by the genes passed on from the parents. Whether selection on a trait brings a heritable response depends on where its variation comes from.[10] In 119 drug-type genotypes grown as clones in one controlled-environment facility, broad-sense heritability averaged 0.79 for the cannabinoids, 0.49 for the number of days to maturity, 0.40 for whole-plant morphology and 0.24 for the morphology of the inflorescences.[8]
Traits of single loci
Sex
Cannabis is normally dioecious. Its sex is carried by a pair of sex chromosomes: females are XX and males XY.[11] In crosses between dioecious hemp plants, sex can be placed on a linkage map as a single marker.[12] The mechanism by which the sex chromosomes set the sex of a plant is the subject of Sex determination in cannabis.
The balance of male and female flowers that a plant actually bears, its sex expression, behaves as a quantitative trait. Monoecious hemp cultivars, which bear both kinds of flower on one plant, are chromosomally XX. Scored at every node from 0 (male flowers only) to 6 (female flowers only), their degree of monoecy averaged 3.36 in the cultivar Uso 31 and 5.70 in Epsilon 68. The differences between cultivars held from one trial to the next.[6] Mapping found five quantitative trait loci (QTLs) for sex expression in each of two dioecious crosses and one monoecious cross. Two of the monoecious cross's QTLs lay in a region matching the sex locus of the dioecious maps.[12] A panel of 123 hemp accessions, grown at three sites in Europe, was scored from predominantly dioecious to predominantly monoecious. Genotype accounted for 69 per cent of the variation in that score.[7] A genome-wide association study of the panel found two QTLs for it, associated with male flowers forming on female plants.[13]
Chemotype
THC and CBD are made in the plant as acids, from a shared precursor, by two related enzymes: THCA synthase and CBDA synthase.[4] When Etienne de Meijer and colleagues crossed plants of pure THC and pure CBD chemotype, every F1 plant had a mixed chemotype. In the F2 progenies, pure CBD, mixed and pure THC plants segregated in the ratio 1:2:1. The authors proposed a single locus, B, with two codominant alleles, BD and BT. They suggested that the two alleles coded for different forms of one synthase.[1] A second model held that the two synthases are separate genes lying close together on a chromosome, one or the other inactivated in drug-type and in hemp plants. It rested on a gene resembling THCA synthase that had been found in hemp.[4]
In a cross between the drug-type strain Purple Kush and the hemp cultivar Finola, mapped in 2019, the THCA synthase gene of Purple Kush and the CBDA synthase gene of Finola lay in large stretches rich in retrotransposons that had almost nothing in common. Finola had no THCA synthase gene, active or not. The CBDA synthase gene lay inside a block of about 40 megabases in which no crossing over was seen among 99 offspring. A single recombination separated the THCA synthase region from the end of that block, so the two genes sit at separate loci. The gene resembling THCA synthase found earlier in hemp proved to code for a third enzyme, CBCA synthase. The arrangement fits neither earlier model in full: the two genes are not forms of one gene at one locus, and hemp carries no inactivated copy of THCA synthase.[4] In a 2021 assembly of the CBD-rich cultivar CBDRx, the synthase genes and pseudogenes lay in tandem arrays near the centromere of one chromosome, where recombination is suppressed. Its authors took this close physical linkage to be the cause of the apparent single-locus inheritance. In a cross between the drug cultivar Skunk No. 1 and the hemp cultivar Carmen, one QTL at the arrays accounted for 92 per cent of the variance in the ratio of THC to CBD.[5]
Jonathan Wenger and colleagues tested a model in which the three chemotype classes correspond to functional and non-functional alleles of CBDA synthase. They genotyped CBDA synthase in 297 feral plants from Minnesota, 20 clinical cultivars supplied by the US National Institute on Drug Abuse and 108 plants of Canadian grain cultivars. Plants homozygous for the non-functional allele had THC-type ratios, homozygotes for the functional allele had CBD-type ratios and heterozygotes had intermediate ones. A test cross among feral plants segregated as codominant Mendelian inheritance predicts. Genotype predicted the ratio in the clinical cultivars and, in plants with more than 0.5 per cent total cannabinoids, in the grain cultivars.[14]
Insensitivity to day length
Cannabis is usually treated as a short-day plant, one that flowers once the nights reach a critical length. Some plants flower whatever the day length, a habit growers call autoflowering. In 2022 Jacob Toth and colleagues showed that it behaves as a single recessive character. In two populations grown under long days, 28 of 88 and 24 of 88 plants flowered, close to the quarter expected for a recessive allele segregating in the second generation of a cross. They named the locus Autoflower1 and mapped it to a small region of chromosome 1.[2]
Markers for Autoflower1 identified the cultivars sold as autoflowering but did not predict photoperiod insensitivity in all the material tested. The authors suggested that the trait may have more than one cause. The trait is often traced to Cannabis ruderalis. Toth and colleagues noted that recent genomic studies do not support the existence of that group and left the origin of Autoflower1 open.[2]
Polygenic traits
Flowering time
Outside the autoflowering habit, flowering time varies by degree. Hemp cultivars differ in their sensitivity to day length.[13] In the 123-accession hemp panel, genotype accounted for 74 per cent of the variation in the start of flowering and 79 per cent in the date of full flowering. The broad-sense heritability of the flowering traits was 0.88 to 0.96. The accessions flowered in much the same order at all three sites.[7] The association study of the same panel found six QTLs for flowering-time traits across environments. Their regions held genes of light perception and signalling and transcription factors known to regulate flowering.[13]
Some loci of large effect also act on flowering time. In the hemp cultivar Umpqua, plants fell into early and late groups in a ratio near 1:1, the pattern of a major gene heterozygous in one parent and homozygous in the other. The locus, Early1, brings flowering forward by two to four weeks. It lies on chromosome 1, at a different place from Autoflower1.[2]
Height and yield
In the hemp panel the environment accounted for more than 60 per cent of the variation in stem diameter, plant height and stem dry weight.[7] In the drug-type genotypes the broad-sense heritability of plant height was 0.52.[8] Patrick Woods and colleagues mapped a cross between the tall, late-flowering fibre cultivar Carmagnola and the short, early grain cultivar USO31 and found 34 QTLs for agronomic traits. Three QTLs explained plant height. Most of the agronomic QTLs fell into four clusters; seed yield, thousand-seed mass and dry biomass each had a single QTL. The authors concluded that a few pleiotropic loci of large effect control much of the agronomic difference between the two cultivars. They contrasted this with the classical model of many loci of small effect.[3]
Cannabinoid content
The total amount of cannabinoid a plant makes is inherited apart from the ratio between THC and CBD. In the Skunk No. 1 × Carmen cross, six QTLs on five chromosomes together accounted for 53 per cent of the variance in total cannabinoid content. None lay at the synthase arrays. Two lay near genes of pathways that supply substrates for cannabinoid synthesis: one, with 17 per cent of the variance, near the gene for acyl-activating enzyme 1, the last enzyme of the hexanoate pathway; another, on the X chromosome, with 9 per cent, near the gene for the last enzyme of the methylerythritol phosphate pathway.[5] An earlier analysis of the same cross had found one locus strongly linked to total cannabinoid content outside the synthase region. On the 2019 map its marker lies close to the gene for aromatic prenyltransferase, the enzyme that makes cannabigerolic acid, the substrate of both synthases.[5][4] Purple Kush carries more than five times as much of that gene's transcript as Finola.[4]
In the Carmagnola × USO31 cross most QTLs for cannabinoids and terpenes fell into two regions that interacted with each other. These epistatic interactions explained between 3.9 and 15.1 per cent of the variance in individual traits, less than the additive effects.[3] The broad-sense heritability of total cannabinoid concentration in the drug-type genotypes was 0.62, within a range of 0.51 to 0.96 for individual cannabinoids.[8] In feral, clinical and grain cannabis, total cannabinoid content varied widely among plants while the ratio of THC to CBD followed their CBDA synthase genotype.[14]
Traits shaped by the environment
The same genotype can express a trait differently in different environments. Where genotypes respond differently from one another to the same change of environment, there is a genotype-by-environment interaction, which can change their order from one environment to the next.[15] In the 123-accession hemp panel, the environment strongly influenced the agronomic traits, the pectin content of the cell walls and most fibre traits. For dry-matter content and some fibre traits the interaction outweighed the genetic effect and the accessions changed rank between sites. Plants grown in the Netherlands were taller and thicker-stemmed and flowered later than at the other two sites, while plants grown in Italy flowered earlier and over a longer period.[7]
In the 119 drug-type genotypes grown as clones, the ratios between cannabinoids stayed fairly stable across the facility while their absolute quantities varied significantly; clones of one genotype differed by 25 to 43 per cent in THC concentration.[8] In six hemp cultivars grown over three years, genotype, year and their interaction accounted for 33.9, 36.5 and 21.4 per cent of the variation in cannabinoids, while year dominated the variation in every other class of metabolite measured in the inflorescences.[16] Petit and colleagues judged traits with large interactions poor targets for hemp breeding, because a selection may behave unexpectedly at sites where it has not been tested.[7]
See also
References
- ↑ 1.0 1.1 de Meijer, E.P.M.; Bagatta, M.; Carboni, A.; Crucitti, P.; Moliterni, V.M.C.; Ranalli, P.; Mandolino, G. (2003). "The inheritance of chemical phenotype in Cannabis sativa L.". Genetics. 163 (1): 335–346. doi:10.1093/genetics/163.1.335.
- ↑ 2.0 2.1 2.2 2.3 Toth, J.A.; Stack, G.M.; Carlson, C.H.; Smart, L.B. (2022). "Identification and mapping of major-effect flowering time loci Autoflower1 and Early1 in Cannabis sativa L." Frontiers in Plant Science. 13 991680. doi:10.3389/fpls.2022.991680.
- ↑ 3.0 3.1 3.2 Woods, P.; Campbell, B.J.; Nicodemus, T.J.; Cahoon, E.B.; Mullen, J.L.; McKay, J.K. (2021). "Quantitative trait loci controlling agronomic and biochemical traits in Cannabis sativa". Genetics. 219 (2) iyab099. doi:10.1093/genetics/iyab099.
- ↑ 4.0 4.1 4.2 4.3 4.4 4.5 Laverty, K.U.; Stout, J.M.; Sullivan, M.J.; Shah, H.; Gill, N.; Holbrook, L.; Deikus, G.; Sebra, R.; Hughes, T.R.; Page, J.E.; van Bakel, H. (2019). "A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci". Genome Research. 29 (1): 146–156. doi:10.1101/gr.242594.118. PMC 6314170.
- ↑ 5.0 5.1 5.2 5.3 Grassa, C.J.; Weiblen, G.D.; Wenger, J.P.; Dabney, C.; et al. (2021). "A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana". New Phytologist. 230 (4): 1665–1679. doi:10.1111/nph.17243. PMC 8248131.
- ↑ 6.0 6.1 Faux, A.-M.; Berhin, A.; Dauguet, N.; Bertin, P. (2014). "Sex chromosomes and quantitative sex expression in monoecious hemp (Cannabis sativa L.)". Euphytica. 196 (2): 183–197. doi:10.1007/s10681-013-1023-y.
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Petit, J.; Salentijn, E.M.J.; Paulo, M.-J.; Thouminot, C.; van Dinter, B.J.; et al. (2020). "Genetic variability of morphological, flowering, and biomass quality traits in hemp (Cannabis sativa L.)". Frontiers in Plant Science. 11 102. doi:10.3389/fpls.2020.00102.
- ↑ 8.0 8.1 8.2 8.3 8.4 Naim-Feil, E.; Elkins, A.C.; Malmberg, M.M.; Ram, D.; Tran, J.; et al. (2023). "The cannabis plant as a complex system: interrelationships between cannabinoid compositions, morphological, physiological and phenological traits". Plants. 12 (3) 493. doi:10.3390/plants12030493.
- ↑ Beavis, W.; Lamkey, K.; Espinosa, K.; Mahama, A.A.; Suza, W. (2023). "Gene Effects". In Suza, W.; Lamkey, K. (eds.). Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. doi:10.31274/isdup.2023.146.
- ↑ Beavis, W.; Lamkey, K.; Espinosa, K.; Mahama, A.A.; Suza, W. (2023). "Components of Variance". In Suza, W.; Lamkey, K. (eds.). Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. doi:10.31274/isdup.2023.146.
- ↑ Divashuk, M.G.; Alexandrov, O.S.; Razumova, O.V.; Kirov, I.V.; Karlov, G.I. (2014). "Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system". PLoS ONE. 9 (1) e85118. doi:10.1371/journal.pone.0085118.
- ↑ 12.0 12.1 Faux, A.-M.; Draye, X.; Flamand, M.-C.; Occre, A.; Bertin, P. (2016). "Identification of QTLs for sex expression in dioecious and monoecious hemp (Cannabis sativa L.)". Euphytica. 209 (2): 357–376. doi:10.1007/s10681-016-1641-2.
- ↑ 13.0 13.1 13.2 Petit, J.; Salentijn, E.M.J.; Paulo, M.-J.; Denneboom, C.; Trindade, L.M. (2020). "Genetic architecture of flowering time and sex determination in hemp (Cannabis sativa L.): a genome-wide association study". Frontiers in Plant Science. 11 569958. doi:10.3389/fpls.2020.569958.
- ↑ 14.0 14.1 Wenger, J.P.; Dabney, C.J.; ElSohly, M.A.; Chandra, S.; Radwan, M.M.; Majumdar, C.G.; Weiblen, G.D. (2020). "Validating a predictive model of cannabinoid inheritance with feral, clinical, and industrial Cannabis sativa". American Journal of Botany. 107 (10): 1423–1432. doi:10.1002/ajb2.1550. PMC 7702092.
- ↑ Beavis, W.; Lamkey, K.; Espinosa, K.; Mahama, A.A.; Suza, W. (2023). "G x E". In Suza, W.; Lamkey, K. (eds.). Quantitative Genetics for Plant Breeding. Iowa State University Digital Press. doi:10.31274/isdup.2023.146.
- ↑ Beleggia, R.; Menga, V.; Fulvio, F.; Fares, C.; Trono, D. (2023). "Effect of genotype, year, and their interaction on the accumulation of bioactive compounds and the antioxidant activity in industrial hemp (Cannabis sativa L.) inflorescences". International Journal of Molecular Sciences. 24 (10) 8969. doi:10.3390/ijms24108969.