Talk:Inbreeding

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Discussion for: Inbreeding • View • Links • Related changes

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Page scope

Inbreeding covers inbreeding as a mating system and its genetic effect: identity by descent and the inbreeding coefficient, systems of mating, selfing and related matings in plants, how inbreeding is read from markers, and where it arises in cannabis. The loss of fitness belongs to Inbreeding depression, the making and use of lines to Inbred line, the definition and values of heterozygosity to Heterozygosity, selfing studies in cannabis to Outcrossing and drift to Genetic drift.

Data verification

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Discussion

Sources

Felsenstein (2019), Theoretical Evolutionary Genetics, chapters V and VI: the inbreeding coefficient, genotype frequencies, kinship, sex linkage, systems of mating, finite populations.
Templeton and Read (1994), in Conservation Genetics: three meanings of the word.
Darwin (1876), The Effects of Cross and Self Fertilisation in the Vegetable Kingdom: pp. 10, 413–414 and 436.
David and colleagues (2007), Molecular Ecology 16: 2474–2487, and Bürkli and colleagues (2017), Heredity 118: 525–533: selfing rates from F_IS and from other estimates. Ritland (2002), Heredity 88: 221–228: biparental inbreeding. Igic and Kohn (2006), Evolution 60: 1098–1103: the distribution of outcrossing rates. Vekemans and Hardy (2004), Molecular Ecology 13: 921–935: fine-scale structure.
Pollak (1987) and Caballero and Hill (1992), Genetics: effective size under partial inbreeding. Nordborg (2000), Genetics, and Szulkin and colleagues (2010), Evolution: linkage disequilibrium.
Keller and colleagues (2011), Genetics; Kardos and colleagues (2015), Heredity; Wang (2016), Theoretical Population Biology; Ceballos and colleagues (2018), Nature Reviews Genetics: pedigree and genomic measures, runs of homozygosity.
Borin and colleagues (2021), Plants; Boutsika and colleagues (2025), PeerJ; Dufresnes and colleagues (2017), PLoS ONE; Aina and colleagues (2025), Scientific Reports; Sawler and colleagues (2015), PLOS ONE: marker surveys of cannabis.
Mansueto and colleagues (2024), BMC Genomics; García-de Heer and colleagues (2024, 2026); Stack and colleagues (2025), International Journal of Molecular Sciences; Punja and Holmes (2020), Frontiers in Plant Science; Ingvardsen and Brinch-Pedersen (2023), Frontiers in Plant Science; van Bakel and colleagues (2011), Genome Biology; Barcaccia and colleagues (2020), Frontiers in Plant Science: selfing and homozygosity in cannabis.

Where the sources disagree

Effective size under partial sib mating. Pollak (1987) gives N/(1 + 3F_IS) for partial full-sib mating with binomial offspring numbers. Caballero and Hill (1992) call the earlier equations for partial sib mating incorrect and give N/(1 + α) for a Poisson distribution of family size.
Borin and colleagues (2021). The text calls F_IS always positive; the per-locus table shows 0.00 at one locus, SSR_6–3.
Dufresnes and colleagues (2017) and Borin and colleagues (2021) both type hemp varieties with microsatellites and differ in mean F_IS, 0.19 against 0.41. The first averages over varieties and the second over loci, with different loci and plants.
Generation labels. Mansueto and colleagues label their inbred lines F₁ to F₄. García-de Heer and colleagues, on a similar panel, label generations S₀ to S₆.

How far the evidence goes

The table of coefficients in "Systems of mating" is calculated from Felsenstein's recurrence equations: (V-24) for selfing, (V-26) and (V-27) for full siblings, (V-42) for double first cousins and (VI-6) for random mating. The long-run values are his: 0.5, 0.809, 0.920 and 1 − 1/(2N). The equations assume no mutation and no selection.
The one-third in "Half selfing therefore gives one third" is the formula s/(2 − s) at s = 0.5. The formula assumes inbreeding equilibrium.
F_IS in the table comes from different marker systems and groupings. Dufresnes and colleagues compute it within varieties, Boutsika and colleagues over two groups each holding many accessions and Aina and colleagues over all plants and within clusters. The values are not one quantity.
The surveys report F_IS and give no selfing rate from progeny arrays for monoecious hemp or any other cannabis. How much seed a monoecious hemp plant sets by its own pollen in a field is not settled by these papers.
The F_IS surveys cover cultivars, breeding material and feral plants of the United States; the hemp set of Dufresnes and colleagues includes European landraces. Whether landrace populations in cultivation hold fewer heterozygotes than Hardy–Weinberg proportions predict is not settled by them.
Keller and colleagues' 6.25 and 2.4 per cent are for human progeny of first cousins. Kardos and colleagues simulated mapped genomes of 20 chromosomes. Neither measures cannabis.
Stack and colleagues describe FL 58 as an inbred line by personal communication. The assembly's runs of homozygosity are consistent with that account.
Sawler and colleagues' two explanations and the suggestion of Ingvardsen and Brinch-Pedersen about illegal production are proposals. None of these papers has pedigree data for drug-type plants.

Terms

Identical by descent: copied from one gene copy in an ancestor. Two copies can be alike without being so, which is identity by state.
Selfing and self-fertilisation: a plant's egg cells fertilised by its own pollen or by pollen of a clone of the plant.
Biparental inbreeding: mating between relatives other than selfing.
F_IS: the shortfall of heterozygotes in a sample against Hardy–Weinberg proportions, (H_E − H_O)/H_E.
F_ROH: the share of a genome inside runs of homozygosity.

Images reserved in the article

Two images have places in the article but are not yet uploaded:

File:Inbreeding-half-sibling-pedigree.jpg (Identity by descent), a diagram to be drawn: a pedigree of a shared parent, two half-siblings and their offspring, with the three steps marked 1/2 and the result f = 1/8.
File:Inbreeding-coefficient-under-systems-of-mating.jpg (Systems of mating), a chart to be drawn from the table in that section: the inbreeding coefficient against generation for selfing, full siblings, double first cousins and random mating in 100 and in 10 plants.