Genetic selection is at the heart of improving the performance of our livestock species. For several decades, breeders have been trying to increase productivity, disease resistance and environmental adaptation by selecting the best individuals. However, an often inevitable consequence of selection is an increase in inbreeding.
A high level of inbreeding can lead to a phenomenon known as inbreeding depression, which has a negative impact on traits of interest such as growth, fertility and feed efficiency.
There are two main approaches to quantifying and managing this phenomenon: one based on parentage information (the pedigree), and the other based on genetic information using genotyping or DNA sequencing tools.
Pedigree-based inbreeding: simple but imperfect
Pedigree inbreeding is calculated from an animal’s pedigree information. It represents the probability that two alleles of a given gene are identical because they come from a common ancestor. Depending on the genealogical information we have on our lines, it is possible to go back several dozen generations of selection to estimate the links between individuals in our lines.
This inbreeding measurement has several advantages:
- Use of historical data: as the genealogical information on our lines has been well documented for a large number of generations, pedigree inbreeding can be monitored over very long periods.
- Simple calculations: since mathematical formulas are relatively straightforward, pedigree inbreeding can be quickly estimated from pedigree data.
- Quickly taken into account in selection: When animals of interest that are too inbred are identified, they can be crossed with other individuals, less inbred, to limit the impact of inbreeding on selection.
On the other hand, pedigree inbreeding measurement also has a number of disadvantages:
- Accuracy limited by the depth of the pedigree: the quality of the estimate depends heavily on the reliability and number of generations for which pedigree information is available. Errors or gaps in pedigree can bias or even falsify the results. For example, if we go back to the earliest ancestors in a given line for which pedigree information is no longer available, the inbreeding rate for these “founder” individuals will be 0.
- Simplifying assumptions: traditional approaches often assume an equal contribution from all parents, whereas genetic transmission can be more complex.
- Failure to detect some genetic variations: the pedigree does not capture variations due to recent mutations or linked to chromosomal recombination events, which may limit the assessment of real genetic diversity.
Genome-based inbreeding: a clearer view of the problem
Using genotyping or DNA sequencing tools, it is possible to identify molecular markers such as SNPs (Single Nucleotide Polymorphism). These SNPs correspond to variations of a nucleotide base of the DNA, very frequent and very regular along the DNA. Available on a large number of markers (several tens of thousands), molecular information can then be used to estimate genomic inbreeding.
Various genomic inbreeding indicators exist, making it possible to estimate the level of inbreeding across the whole genome, but also according to regions of the genome, according to chromosomes or even according to zones on chromosomes. For example, it is possible to identify regions of the genome where there is no genetic variation between individuals. These are known as regions of prolonged homozygosity (or ROHs for “Runs of Homozygosity”). Depending on the size of these regions, it is possible to identify conserved regions, with no genetic variation, of varying ages.
Genomic inbreeding measurements have a number of advantages:
- Greater inbreeding accuracy: genomic data provides access to molecular information on a large number of genetic markers, giving a more detailed picture of actual inbreeding.
- Better differentiation between related individuals: it becomes possible to differentiate between two full brothers or sisters based on alleles inherited from their parents, whereas with the pedigree these animals have the same level of inbreeding. This makes it possible to select the most interesting individuals within the same sibling.
- Detection of ‘hidden’ inbreeding: genomic inbreeding indicators make it possible to identify levels of inbreeding that are not apparent in pedigrees, for example for founder animals of our lines, or in the case of errors or incompleteness in historical data.
- Improved understanding of genetic impacts: by precisely identifying the regions of the genome affected, it will be possible to study the impact of inbreeding on traits of interest and optimise population management.
But like pedigree inbreeding, these measures also have their drawbacks:
- Higher cost: genomic analyses (particularly full sequencing) are still expensive and require computer tools and specific bioinformatics skills.
- A multitude of genomic inbreeding indicators: different indicators exist for estimating genomic inbreeding levels, with no real scientific consensus on the most interesting indicator to use. For the same population, these indicators are more or less correlated with each other.
- Complex interpretation: Depending on the indicators used, interpreting the results may require an in-depth understanding of genetic dynamics.
- Partial or biased molecular information: Genotyping chips used routinely do not cover all molecular variations in the genome of our ducks. Although they have been optimised to consider all regions of the genome, it is possible for certain regions of the genome without any variation not to be detected.
Pedigree inbreeding and genomics: two complementary approaches
Comparative studies show that inbreeding coefficients calculated from pedigrees and those derived from genomic data are often correlated but may diverge depending on the depth of pedigree and the quality of molecular data. In some cases, for example, it is even possible to observe a negative correlation between pedigree inbreeding and some genomic inbreeding indicators. This is very often linked to the fact that, even if pedigree data goes back a large number of generations, founder animals also have a certain history which may itself be very old.
However, for selection lines for which pedigree data are old, the different inbreeding indicators, pedigree and genomic, remain positively correlated. These two approaches therefore complement each other.
The consequences of inbreeding on selection
Inbreeding, whether pedigree or genomic, has a direct impact on the effectiveness and sustainability of selection programmes. The accumulation of homozygosity in the genome, as a result of crosses between related individuals, can lead to inbreeding depression, resulting in reduced performance in traits of interest such as fertility, growth or disease resistance. These negative effects are particularly critical in breeding for highly selected lines, where genetic diversity can be quickly reduced.
If individuals become genetically too similar, this will result in a reduction in genetic variability. In the long term, this limits the possibilities of choosing breeding animals with new or favourable genetic combinations. Yet this genetic variability is one of the driving forces behind genetic progress. If variability were to be reduced too much, the result would be a reduction in genetic progress. It is therefore essential for the breeder to pay attention to the levels of inbreeding of selected individuals and to matings carried out between selected individuals.
Inbreeding measurements therefore play a crucial role in the management of matings. When molecular information is not available, pedigree inbreeding can be taken into account to avoid crosses between individuals that are too closely related. But with genomic tools, it is possible to go further: we can identify precisely the problematic regions of the genome and integrate this information into selection algorithms, to minimise genomic inbreeding while maximising genetic progress.
CONCLUSION
In short, taking inbreeding into account – not only as a value to be monitored, but also as a criterion to be integrated into selection – is becoming essential if we are to reconcile genetic improvement and the preservation of diversity in our breeding lines. Together, pedigree and genomic tools will enable us to better control crossbreeding, avoid excessive inbreeding and preserve genetic diversity, which is a guarantee of robustness and resilience in the face of future breeding challenges.
