Biology subjects

Rupp, R.

Publications and source records attributed to Rupp, R..

5 recordsLinked to original sources

bioRxiv2025

Genome landscape and genetic architecture of recombination in domestic goats (Capra Hircus)

BackgroundRecombination is a fundamental biological process, both in participating to the creation of viable gametes and as a driver of genetic diversity. Characterising recombination is therefore of strong interest in breeding populations. In this study, we used [~]50K genotyped data and pedigree from two French populations (Alpine and Saanen) of domestic goats (Capra hircus) to build sex-specific recombination maps, and to explore the genetic basis of two recombination phenotypes: genome-wide recombination rate (GRR) and intra-chromosomal shuffling. ResultsSex-specific recombination maps showed higher recombination in males than females for both breeds (Alpine autosomal map size = 35.1M in males and 30.5M in females; Saanen map size = 34.0M in males and 29.0M in females). Heterochiasmy is particularly notable on small chromosomes, and at both ends of the chromosomes. Yet, no difference in shuffling has been found between populations. Genetic parameters on recombination phenotypes could only be estimated in males, due to lack of data in females. Both phenotypes are significantly heritable (h{superscript 2}=0.12 (0.03) for GRR and h{superscript 2}=0.034 (0.015) for shuffling, when pooling breeds). GWAS on male GRR identified several significant loci, including RNF212, RNF212B and SSH1, the last one being a novel locus for this phenotype. Correlation of SNP effects between breeds is low for both recombination phenotypes (0.25 for GRR and 0.04 for shuffling), indicating different genetic determinants in the two breeds. ConclusionsThis study contributes to the understanding of recombination evolution in ruminants, both between breeds and species.

genetics↗

bioRxiv2024

SMARTER-database: a tool to explore genomic diversity in small ruminants

Underutilized sheep and goat breeds have the ability to adapt to challenging environments due to their genetic composition. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by important data discrepancies, such as outdated assembly versions or different data formats. Here we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata mainly from SNP chips arrays on global small ruminant populations with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via FTP and interact with the metadata through a web interface or programmatically using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database. Availability & ImplementationThe code is available as open source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database.

bioinformatics↗

bioRxiv2020

Analysis Of Polycerate Mutants Reveals The Evolutionary Co-Option Of HOXD1 To Determine The Number And Topology Of Horns In Bovidae

In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as headgear, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

genomics↗

bioRxiv2020

Mitotic activity shapes stage-specific histone modification profiles during Xenopus embryogenesis

Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harnish developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S-transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle-arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles, in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted back towards normality on morphological, molecular and epigenetic levels. These results indicate that replicational dilution of histone marks has a strong impact on developmental chromatin maturation. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.

molecular biology↗

bioRxiv2020

Computational modeling reveals cell-cycle dependent kinetics of H4K20 methylation states during Xenopus embryogenesis

Histone modifications regulate chromatin architecture and thereby control gene expression. Rapid cell divisions and DNA replication however lead to a dilution of histone modifications and can thus affect chromatin mediated gene regulation So how does the cell-cycle shape the histone modification landscape, in particular during embryogenesis when a fast and precise control of cell-specific gene expression is required? We addressed this question in vivo by manipulating the cell-cycle during early Xenopus laevis embryogenesis. The global distribution of un-, mono- di- and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific methylation rate constants were required to explain the measured H4K20 methylation state kinetics. Interestingly, demethylation was found to be redundant in the cycling embryos but essential in the cell-cycle arrested embryos. Together, we present the first quantitative analysis of in vivo histone H4K20 methylation kinetics. Our computational model shows that demethylation is only essential for regulating H4K20 methylation kinetics in non-cycling cells. In rapidly dividing cells of early embryos, we predict that demethylation is dispensable, suggesting that cell-cycle mediated dilution of chromatin marks is an essential regulatory component for shaping the epigenetic landscape during early embryonic development.

bioinformatics↗