Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
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 mainte...
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2024-10-01
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| author | Bortoluzzi, Chiara Restoux, Gwendal Rouger, Romuald Desnoues, Benoit Petitjean, Florence Bosse, Mirte Tixier-Boichard, Michèle |
| author_facet | Bortoluzzi, Chiara Restoux, Gwendal Rouger, Romuald Desnoues, Benoit Petitjean, Florence Bosse, Mirte Tixier-Boichard, Michèle |
| author_sort | Bortoluzzi, Chiara |
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| description | 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 (Δπ), deleterious variation (ΔL), and inbreeding (ΔF) 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. |
| format | Article |
| id | doaj-art-a16e613acd1b43189f093a2fd8239ae2 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Peer Community In |
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| series | Peer Community Journal |
| spelling | doaj-art-a16e613acd1b43189f093a2fd8239ae22025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-10-01410.24072/pcjournal.47410.24072/pcjournal.474Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds Bortoluzzi, Chiara0https://orcid.org/0000-0001-6589-6635Restoux, Gwendal1https://orcid.org/0000-0001-7771-9476Rouger, Romuald2https://orcid.org/0000-0002-7227-4719Desnoues, Benoit3Petitjean, Florence4Bosse, Mirte5https://orcid.org/0000-0003-2433-2483Tixier-Boichard, Michèle6https://orcid.org/0000-0001-5944-7884Wageningen University & Research - Animal Breeding and Genomics, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, FranceUniversité Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, FranceCentre INRAE Val de Loire, UMR-BOA, SYSAAF, 37380 Nouzilly, FranceSyndicat des Selectionneurs Avicoles et Aquacoles Français (SYSAAF), Unité Mixte de Recherche-UMR Biologie des Oiseaux et Aviculture-BOA, Val de Loire, 37380, Nouzilly, FranceCentre de Sélection de Béchanne, Hameau de Béchanne, 01370 Saint-Etienne-Du-Bois, FranceVU University - Amsterdam Institute for Life and Environment (A-LIFE), De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; Wageningen University & Research - Animal Breeding and Genomics, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsUniversité Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, FranceLivestock 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 (Δπ), deleterious variation (ΔL), and inbreeding (ΔF) 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.https://peercommunityjournal.org/articles/10.24072/pcjournal.474/Conservation program, Inbreeding, Genetic diversity, Genetic load, Chicken |
| spellingShingle | Bortoluzzi, Chiara Restoux, Gwendal Rouger, Romuald Desnoues, Benoit Petitjean, Florence Bosse, Mirte Tixier-Boichard, Michèle Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds Peer Community Journal Conservation program, Inbreeding, Genetic diversity, Genetic load, Chicken |
| title | Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
|
| title_full | Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
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| title_fullStr | Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
|
| title_full_unstemmed | Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
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| title_short | Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
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| title_sort | trends in genome diversity of small populations under a conservation program a case study of two french chicken breeds |
| topic | Conservation program, Inbreeding, Genetic diversity, Genetic load, Chicken |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.474/ |
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