Biology subjects

Tixier-Boichard, M.

Publications and source records attributed to Tixier-Boichard, M..

7 recordsLinked to original sources

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↗

bioRxiv2023

Reintroducing genetic diversity in populations from cryopreserved material: The case of Abondance, a French local dairy cattle breed

BackgroundGenetic diversity is a necessary condition for populations to evolve under adaptation, selection or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources appear as a promising option to reintroduce lost variants and to limit inbreeding. However, while more common in plant breeding, the use of cryopreserved resources is less documented in animals due to a longer generation interval making it difficult to fill the performance gap due to continuous selection. Thus, this study investigates one of the only concrete cases presenting the results of the use of cryopreserved semen of a bull born in 1977 and belonging to a disappeared lineage, into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later. ResultsWe found that this re-used bull was very original relative to the current population and thus allowed to restore genetic diversity lost over time. The expected negative gap in milk production due to continuous selection has been absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this old bull did not increase the level of inbreeding, it even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of an old bull in the breeding scheme allowed for increased performance for reproductive abilities, a trait that was less subject to selection in the past. ConclusionsThe use of cryopreserved material was efficient to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid toward mating in order to limit the disadvantages associated with the provision of genetic originality, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, a careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations and of local or small ones in particular. These results could also be transferred to the conservation of wild 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↗

bioRxiv2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

BackgroundFunctional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).\n\nResultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.\n\nConclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

genomics↗