Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breedsuse asterix (*) to get italics

Chiara Bortoluzzi, Gwendal Restoux, Romuald Rouger, Benoit Desnoues, Florence Petitjean, Mirte Bosse, Michele Tixier-BoichardPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2024

<p>Livestock biodiversity is declining globally at rates unprecedented in human history. Of all avian species, chickens are among the most affected ones because many local breeds have a small effective population size that makes them more susceptible to demographic and genetic stochasticity. The maintenance of genetic diversity and control over genetic drift and inbreeding by conservation programs are fundamental to ensure the long-term survival and adaptive potential of a breed. However, while the benefits of a conservation program are well understood, they are often overlooked. We here used temporal whole-genome sequencing data to assess the effects of a conservation program on the genetic diversity (∆π), deleterious variation (∆L), and inbreeding (∆F) of two local French chicken breeds, the Barbezieux and Gasconne. We showed that when the conservation program is consistent over time and does not undergo any major organisational changes (i.e., Barbezieux), the loss of genetic diversity is limited. This was true for both pedigree and genomic inbreeding but also for the genetic load estimated from functionally important genome-wide variants. However, when a conservation program is interrupted or re-initiated from scratch (i.e., Gasconne), the loss of genetic diversity can hardly be limited as a result of the bottleneck effect associated with the re-sampling. Our results reinforce the imperative to establish and sustain existing conservation programs that aim to keep populations with a relatively small effective population size from the brink of extinction. Moreover, we conclude by encouraging the use of molecular data to more effectively monitor inbreeding at the genome level while improving fitness by tracking protein-coding and non-coding deleterious variants.</p>

https://www.ebi.ac.uk/ena/browser/view/PRJEB72503You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

https://doi.org/10.5281/zenodo.12744831You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

https://doi.org/10.5281/zenodo.12744831You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Conservation program, Inbreeding, Genetic diversity, Genetic load, Chicken

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Bioinformatics, Evolutionary genomics, Population genomics, Vertebrates

Hernan Morales Villegas [hernanm@sund.ku.dk] suggested: Hi, I would love to review for PCI so please keep me in mind. However, I have active collaborations with two authors so there is a conflict of interest. , Hernan Morales Villegas [hernanm@sund.ku.dk] suggested: You could try:, Hernan Morales Villegas [hernanm@sund.ku.dk] suggested: Christina Hvilsom <CH@zoo.dk>; Claudia Fontsere Alemany <claudia.fontsere@sund.ku.dk>; Patrícia Chrzanová Pecnerová <patricia.pecnerova@bio.ku.dk>; Linett Rasmussen <lras@zoo.dk>, Markus Neuditschko suggested: Bortoluzzi et al., assessed various genetic diversity parameters of two local French Chicken breeds taking advantage of whole-genome sequencing information. The study is well-written and easy to follow. However, I have some major concern about the small sample size, as they only analyzed 15 samples for each time period (2003 and 2013). To better assess the selected sample size, authors should also provide more information about the breeds (e.g. the number of registered animals in the pedigree). Furthermore, the authors did not provide any information, how the 15 animals were selected. Based on pedigree information, it is possible to select most informative individuals by assessing their marginal gene contribution. Besides, that I have also identified some minor issues:, Markus Neuditschko suggested: L27: replace still in existence with current livestock populations, Markus Neuditschko suggested: L43: Livestock breeders instead of keepers, Markus Neuditschko suggested: L45: routinely implemented, Markus Neuditschko suggested: L97: robust and generally, Markus Neuditschko suggested: Figure 1b: The PCA visualization is not quite informative, as the points are colored according to the time point and not to breed origin. To increase the visualization of the PCA, I suggest to use different shapes (time point) and colors (breeds). Also the variance explained by the first two components is rather low, hence it might also be informative to explore additional components., Markus Neuditschko suggested: L459: The authors mentioned, that the breeds were previously genotyped on 57K SNP chip data and simultaneously highlight the added value of genome sequencing data. To do so, I would suggest to downsize sequencing data to 57K Data, to confirm the arguments posted in this section.

e.g. John Doe john@doe.com

No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2024-02-26 13:01:08

Claudia Kasper