Biology subjects

Rochus, C. M.

Publications and source records attributed to Rochus, C. M..

3 recordsLinked to original sources

bioRxiv2025

Review: Estimates of livestock genetic diversity in the UK

The United Kingdom is home to many local and rare livestock breeds. The local breed populations are highly adapted to specific environments in the United Kingdom and these and other rare breeds provide solutions to niche needs. Rare breeds often contribute more than expected to overall species genetic diversity, which is important because genetic variation is needed for adapting to new challenges. It is therefore very important from both United Kingdom and global perspectives to maintain genetic diversity of rare livestock breeds in the United Kingdom, and to do this, we need to evaluate the monitoring of genetic diversity to identify gaps in our knowledge and prioritise resources reserved for conservation purposes. The objectives of this study were to survey the literature to: (1) summarise genetic/genomic characterisation (effective population size (Ne) and inbreeding) of domestic populations (livestock and equine) in the United Kingdom and Ireland; (2) compare number of populations on the United Kingdoms Rare Breeds Survival Trust watch list and the number of United Kingdom and Irish populations in the peer-reviewed literature with inbreeding, genetic diversity and/or Ne estimates; and (3) compare annually reported (census-based) estimates of Ne with (inbreeding- and DNA-based) estimates from peer-reviewed literature. We found a total of 37 publications with Ne or inbreeding estimates for United Kingdom or Ireland livestock populations, published from 1975 to 2024. While many (42%) of the breeds on the Rare Breeds Survival Trust watchlist have been included in publications, there are still many breeds, and a few species (turkey, duck and geese) with no publicly available pedigree- or DNA-based genetic diversity measures. We found census-based Ne estimates were, on average, higher than DNA-based estimates, likely due to violated assumptions when estimating Ne with census-based data because of the way livestock mating systems are designed. Most peer-reviewed papers estimated genetic diversity measures using pedigree, microsatellite markers, or single nucleotide polymorphisms (SNP) markers. To identify breed-unique variants responsible for adaptive traits in rare breeds, more studies using whole-genome sequencing will be needed. Altogether, we have summarised genetic diversity estimates of United Kingdom livestock populations, identifying gaps in knowledge. ImplicationsMaintaining genetic diversity in livestock helps safeguard against future challenges to our food production systems. We surveyed publicly available measures of genetic diversity for farm animal populations in the United Kingdom (including government, Rare Breeds Survival Trust, and peer-reviewed scientific publications) to identify any gaps. We found census-based estimates of genetic diversity, which are used to inform and prioritise resources for conservation efforts, on average, are likely overestimating available genetic diversity. Additionally, most farm animal breeds had only these census-based estimates. Genetic diversity estimates could be improved using pedigree or DNA information, more accurately identifying endangered breeds.

genetics↗

bioRxiv2019

A chromosome-level assembly of the Atlantic herring - detection of a supergene and other signals of selection

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo PacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.

genomics↗

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↗