Inbreeding and epigenetics: beneficial as well as deleterious effects

The correspondence article by Christian Biémont (Biémont, C. Inbreeding effects in the epigenetic era. Nature Rev. Genet. 11, 234 (2010)1 and the articles (Charlesworth, D. & Willis, J. H. The genetics of inbreeding depression. Nature Rev. Genet. 10, 783–796 (2009)2,3 he discusses deserve further dialogue. These papers summarized the theoretical basis of inbreeding depression, defined as the deleterious effects that result from crossing related individuals. Rather than this phenomenon being the result of DNA sequence alterations, Biémont puts forth a strong argument1 that inbreeding depression probably results from epigenetic mechanisms — that is, chromosomal events in which DNA sequence is not altered. Epigenetic mechanisms include cell-specific DNA hyper- and hypomethylation4, RNA interference5, histone modifications6, chromatin remodelling7 and canalization/decanalization8.

Our laboratory has observed the opposite of inbreeding depression — that is, 'inbreeding de-repression'. This can be defined as the beneficial effects that result from crossing related individuals. By inbreeding a freshly generated knockout mouse line, we found that subsequent generations produced much healthier viable offspring compared with the F1 generation.

Cytochrome P450 genes, or at least those members in the Cyp1, Cyp2, Cyp3 and Cyp4 gene families9, are commonly perceived as liver enzymes that metabolize drugs and environmental chemicals. However, most if not all of the CYP1 to CYP4 enzymes exist in many cell types and have important endogenous roles. Among other functions, these enzymes participate in eicosanoid synthesis and/or degradation9,10 and therefore are probably crucial upstream determinants of innumerable cellular processes, from vascular or airway constriction/relaxation to tumour progression and cancer metastasis10.

Our laboratory generated the Cyp1a1–Cyp1a2–Cyp1b1−/− triple-knockout mouse by crossing various combinations of female versus male Cyp1a1–Cyp1a2+/− double-knockout heterozygotes with Cyp1b1+/− single-knockout heterozygotes. From 150 F1 litters examined, 58 Cyp1a1–Cyp1a2–Cyp1b1−/− pups survived to birth, and only two females and one male lived to adulthood and were able to breed successfully11. Incomplete-penetrance phenotypes seen in the F1 generation included embryolethality, slower weight gain, hydrocephalus, hermaphroditism and cystic ovaries11. All of these phenotypes are consistent with eicosanoid-mediated processes10,11.

Most intriguingly, as we continued to breed the triple-knockout F1 homozygote survivors, the embryolethality, the lower weight and all of the above-mentioned birth defects disappeared quickly. We believe that these findings represent the action of natural selection — that is, only the healthiest animals survived and were able to breed the subsequent generation. Because this inbreeding de-repression phenomenon happened within just two to four generations, we presume it reflects epigenetic rather than genetic changes in the genome. Although we suspect this also has occurred with other knockout mouse lines, we are not aware of this ever having been reported.

In conclusion, inbreeding can lead not only to depression but also to an improved, healthier, viable phenotype. And, in all likelihood, both deleterious and beneficial traits that appear during brother–sister inbreeding are caused by epigenetic rather than genetic mechanisms.


  1. 1

    Biémont, C. Inbreeding effects in the epigenetic era. Nature Rev. Genet. 11, 234 (2010).

    Article  Google Scholar 

  2. 2

    Charlesworth, D. & Willis J. H. The genetics of inbreeding depression. Nature Rev. Genet. 10, 783–796 (2009).

    CAS  Article  Google Scholar 

  3. 3

    Kristensen, T. N., Pedersen, K. S., Vermeulen, C. J. & Loeschcke, V. Research on inbreeding in the 'omic' era. Trends Ecol. Evol. 25, 44–52 (2009).

    Article  Google Scholar 

  4. 4

    Zuo, T., Tycko, B., Liu, T. M., Lin, H. J. & Huang, T. H. Methods in DNA methylation profiling. Epigenomics 1, 331–345 (2009).

    CAS  Article  Google Scholar 

  5. 5

    Mohr, S., Bakal, C. & Perrimon, N. Genomic screening with RNAi: results and challenges. Annu. Rev. Biochem. 79, 37–64 (2010).

    CAS  Article  Google Scholar 

  6. 6

    Mosammaparast, N. & Shi, Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu. Rev. Biochem. 79, 155–179 (2010).

    CAS  Article  Google Scholar 

  7. 7

    Ho, L. & Crabtree, G. R. Chromatin remodelling during development. Nature 463, 474–484 (2010).

    CAS  Article  Google Scholar 

  8. 8

    Gibson, G. Decanalization and the origin of complex disease. Nature Rev. Genet. 10, 134–140 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Nebert, D. W. & Russell, D. W. Clinical importance of the cytochromes P450. Lancet 360, 1155–1162 (2002).

    CAS  Article  Google Scholar 

  10. 10

    Nebert, D. W. & Karp, C. L. Endogenous functions of the aryl hydrocarbon receptor (AHR): intersection of cytochrome P450 1 (CYP1) metabolized eicosanoids and AHR biology. J. Biol. Chem. 283, 36061–36065 (2008).

    CAS  Article  Google Scholar 

  11. 11

    Dragin, N., Shi, Z. Q., Madan, R., Karp, C. L., Sartor, M. A., Chen, C., Gonzalez, F. J. & Nebert, D. W. Phenotype of the Cyp1a1/1a2/1b1(−/−) triple-knockout mouse. Mol. Pharmacol. 73, 1844–1856 (2008).

    CAS  Article  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Daniel W. Nebert.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nebert, D., Gálvez-Peralta, M., Shi, Z. et al. Inbreeding and epigenetics: beneficial as well as deleterious effects. Nat Rev Genet 11, 662 (2010).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing