Biology subjects

Restoux, G.

Publications and source records attributed to Restoux, G..

8 recordsLinked to original sources

bioRxiv2025

Impact of genomic selection on genetic diversity in five local European cattle breeds

Genomic selection (GS) has revolutionised animal breeding and accelerated genetic gains in breeding programs. While GS has become common in major dairy cattle breeds, its implementation in local breeds has begun only more recently or is still in progress. However, the introduction of GS in some major breeds has also been associated with increased inbreeding rates, raising concerns about the potential effects of GS on the genetic diversity in smaller or local breeds. Our aim was to investigate the impact of GS on genetic diversity in five (small) local cattle breeds from three European countries. The five breeds evaluated were: MRY (from the Netherlands), Norwegian Red (from Norway), Abondance, Tarentaise, and Vosgienne (from France). We investigated changes in population demographic structure, as well as trends and rates of kinship and inbreeding, using both pedigree- and genomic-based measures. The population size varied depending on the breed, with Vosgienne being the smallest and Norwegian Red being the largest. The dataset included 4,645 MRY, 193,489 Norwegian Red, 16,427 Abondance, 8,882 Tarentaise, and 4,466 Vosgienne genotyped animals for more than 40,000 single-nucleotide polymorphisms. Overall, following the implementation of GS in these breeds, we observed a reduction in generation intervals for sires, fewer calves that later became sires, and, for the French breeds, a broader sire usage. Such changes were likely due to GS enabling the preselection and screening of more young bulls. Additionally, we observed a more balanced contribution of the top ten sires after the introduction of GS. Although changes in inbreeding and kinship rates occurred after the introduction of GS, there was no consistent pattern across breeds: rates increased in MRY and Tarentaise, but decreased in Norwegian Red, Abondance, and Vosgienne. Our study suggests that changes and increases in inbreeding rates may occur after the introduction of GS, although they may not be directly due to the introduction of GS per se, but rather due to population management strategies, such as optimal contribution selection or other breeding practices implemented at the nucleus level. Our findings emphasise the importance of monitoring changes in both genetic diversity and population demographic structure after implementing GS in local breeds, as well as adjusting breeding strategies when needed to ensure long-term sustainability. Interpretive SummaryGenomic selection (GS) has transformed cattle breeding. We investigated changes in population demographic structure and genetic diversity in five European breeds after the introduction of GS. Changes in inbreeding and kinship rates were not consistent across breeds, with both increases and decreases observed. Genetic management strategies, such as optimal contribution selection, had a greater impact on maintaining genetic diversity than the introduction of GS per se. These findings highlight the need to monitor changes in genetic diversity and population demographic structure after the implementation of GS and, when needed, to adapt management strategies to ensure long-term sustainability.

genetics↗

bioRxiv2025

Managing the genetic diversity of animal populations using cryobanks: optimizing the constitution of ex situ collection?

To compensate for the erosion of genetic variability taking place in local breeds as well as in large breeds under selection, many countries have set up cryopreserved collections. Currently, there are as many sampling strategies as there are cryobanks. The aim of our study was to examine some parameters for optimizing the constitution of a gene bank. ResultsWe simulated different breeding scenarios of animal populations (i.e. selection or conservation) and examined the impact of using cryopreserved collections according to (i) the size and age of collections or (ii) the sampling strategy to set up these collections. The age of cryopreserved resources was the predominant factor of use in populations under selection, where the use of recently collected sires was favored. For populations under conservation, older reproductive material becomes highly relevant. Using a large number of old individuals enabled better management of matings and helped to slow down the increase in inbreeding on the long term, while the use of a lower number of old individuals enabled some genetic progress to be maintained. Since a gene bank needs to address the needs of all types of populations, continuous enrichment of collections appeared to be a relevant option. In addition, the use of OCS can help to efficiently mobilize ex situ genetic resources in animal breeding programs. ConclusionsCryopreserved genetic resources are an invaluable help in the management of domestic populations. Relevant recommendations for the management of cryopreserved collections can be made according to breeding programs.

genetics↗

bioRxiv2024

Optimizing the use of cryopreserved genetic resources for the selection and conservation of animal populations

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSGenetic diversity is essential for the sustainability and adaptability of populations, and is thus a central pillar of the agro-ecological transition. However, within a population it is inevitable that some amount of genetic variability is lost, and efforts must be made to limit this as much as possible. A valuable tool in this endeavor could be the use of cryopreserved genetic resources in cryobanks, which could assist in the management of various animal populations in the contexts of both selection and conservation. ResultsWe performed simulations that revealed that the most appropriate use of ex situ genetic resources differs radically depending on characteristics of the target population and its management objectives. With populations under conservation, the aim is the management of genetic diversity, which was optimized by the regular use of cryopreserved genetic resources at each generation. For populations under selection, instead, the concern is the addition of additive genetic variability, which benefited from the use of cryopreserved collections over only a few generations based primarily on the genetic values of donors. In both cases, the use of cryopreserved individuals in animal populations requires a large amount of material: for breeds under selection because the number of offspring is high, and for breeds under conservation because the frozen semen is used repeatedly over a long period. ConclusionsThe use of cryopreserved material appears to be an effective means of managing the genetic variability of an animal population, either by slowing down the erosion of variability or by helping to redirect a selection objective. However, care must be taken with populations under selection to limit the disadvantages associated with the reintroduction of old genetic material, in particular the gap in breeding values for traits of interest. Finally, our study highlights the need for a sufficiently large stock of cryopreserved material in collections (e.g., number of doses, straws) to ensure the most efficient use.

genetics↗

bioRxiv2024

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 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 ({Delta}{pi}), deleterious variation ({Delta}L), and inbreeding ({Delta}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.

genomics↗

bioRxiv2023

Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank

Through a combination of selective pressure and genetic drift, there has been a notable erosion of genetic diversity in domesticated animal populations. In response, many countries, including France, have developed gene banks in order to conserve reproductive genetic material. Cryopreserved resources can potentially be used to manage the genetic diversity of populations, but this opportunity is seldom exploited. As an initial step toward this goal, we describe here a methodology for the characterization of the genetic diversity of cryopreserved collections. Using the example of the French National Cryobank, this study employs newly proposed biodiversity metrics to conduct a detailed assessment of the status of collections for six livestock species: cattle, sheep, goat, horse, donkey, and pig. Both the amount of resources available and their characteristics varied among species and/or breeds. Overall, breeds with a large commercial distribution had more donors in the collection than local breeds, while the number of doses available was mainly determined by the physiology of the species. An adapted version of the Gini-Simpson equitability index revealed an unbalanced number of donors between breeds for some species. Similarly, estimates of effective donor numbers (De) highlighted the unequal distribution of donors within a breed. Finally, we developed a new index of diversity impact (IDI) to assess the potential of a collection to reintroduce genetic diversity in contemporary populations. The IDI was calculated on the basis of pedigree data for 17 breeds of three livestock species, pig, sheep, and cattle, which differed in both population size and management program. IDI values are negative when the use of cryoconserved sires would decrease the overall kinship of the current population and positive when it would increase it, enabling the most interesting donors to be chosen for immediate use. Negative (favorable) IDI values 41 were found for both local breeds as well as for commercial populations. In general, older collections exhibited better IDI values but recently collected donors could also be useful for populations undergoing strong selection. Within a breed, IDI can be computed individually and thus be used to select the best sires for a given objective. In the absence of pedigree data, IDI values could also be calculated on the basis of marker genotypes. Overall, this study proposes a framework for the assessment of germplasm collections in the service of various objectives. Compared to FAO indicators motivated by breed reconstitution, the Gini-Simpson and De indices can help to plan sampling more efficiently, whereas IDI can guide donor selection in order to manage the diversity of existing populations. These indicators can be calculated at regular intervals to support the planning and management of collections at national and international levels and help population managers to exploit the resources currently available.

genetics↗

bioRxiv2022

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

Evolutionary processes leave footprints across the genome over time. Highly homozygous regions may correspond to positive selection of favourable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed 176 genomes coming from 20 sequenced US fish and 156 fish from three different French lines that were genotyped using a HD Axiom Trout Genotyping 665K SNP Array. Using methods based on either Run of Homozygosity or Extended Haplotype Homozygosity, we detected selection signals in four domesticated rainbow trout populations. Nine genomic regions composed of 253 genes, mainly located on chromosome 2 but also on chromosomes 12, 15, 16, and 20, were identified under positive selection in all four populations. In addition, four heterozygous regions containing 29 genes putatively under balancing selection were also shared by the four populations and located on chromosomes 10, 13, and 19. Whatever the homozygous or heterozygous nature of the region, we always found some genes highly conserved among vertebrates due to their critical roles in cellular and nuclear organisation, embryonic development or immunity. We identify new promising candidate genes involved in rainbow trout fitness, as well as genes already detected under positive selection in other fishes (auts2, atp1b3, zp4, znf135, igf-1, brd2, col9a2, mrap2, pbx1, emilin-3). These findings represent a genome-wide map of signatures of selection common over rainbow trout populations, which is the foundation to understand the processes in action and to identify what kind of diversity should be preserved, or conversely avoided in breeding programs, in order to maintain or improve essential biological functions in domesticated rainbow trout populations.

genetics↗

bioRxiv2021

Management programs as a key factor for genetic conservation of small populations : The case of French local chicken breeds

On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, for animal production in particular. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds are likely to harbor unique adaptive features and represent a key component of diversity to reach resilience. Nevertheless, they are often suffering from small population size putting these valuable resources at risk of extinction. In chickens, management programs have been initiated a few decades ago in France, relying on a particular niche market aiming at promoting and protecting local breeds. We conducted a unique comprehensive study of 23 French local populations, along with 4 commercial lines, to evaluate their genetic conservation status and the efficiency of management programs. Using a 57K SNP chip we demonstrated that both between and within breeds genetic diversity were high in French populations. Diversity was mainly structured according to selection and breeds history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers practices in terms of exchange, leading to more or less isolated flocks. Analysing demographic parameters as well as molecular information, we showed the efficiency of consistent management programs to conserve genetic diversity, since the earlier the breeds integrated programs the lower was the inbreeding. Finally we stressed that management programs can benefit from molecular markers and runs of homozygosity, ROH, in particular, as a valuable and affordable tool to monitor genetic diversity of local breeds which often lack pedigree information.

genetics↗

bioRxiv2017

High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci

Sheep was one of the first domesticated livestock species in the Anatolia region of contemporary Iran and eventually spread world-wide. Previous studies have shown that French sheep populations likely harbour a large part of European domesticated sheep diversity in a relatively small geographical region, offering a powerful model for the study of adaptation. We studied the diversity of 27 French sheep populations by genotyping 542 individuals for more than 500 000 SNPs. We found that French sheep breeds were divided into two main groups, corresponding to northern and southern origins and additionally we identified admixture events between northern and southern populations. The genetic diversity of domesticated animals results from adaptation of populations to constraints imposed by farmers and environmental conditions. We identified 126 genomic regions likely affected by selection. In many cases, we found evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. Some of these regions harbour genes potentially involved in morphological traits (SOCS2, NCAPG/LCORL, MSRB3), coat colour (MC1R) and adaptation to environmental conditions (ADAMTS9). Closer inspection of two of these regions clarified their evolutionary history: at the LCORL/NCAPG locus we found evidence for introgression of an adaptive allele from a southern population into northern populations and by resequencing MC1R in some breeds we confirmed different mutations in this gene are responsible for the same phenotypic trait. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

genetics↗