Biology subjects

Bean, T.

Publications and source records attributed to Bean, T..

3 recordsLinked to original sources

bioRxiv2026

A dual-clam species 63K SNP array for sustainable production and conservation of wild resources

Bivalves play an essential role in coastal ecosystems and their aquaculture represents an important economic sector in Europe playing a pivotal role within the EU Blue Growth Strategy. Among clam species, the Manila clam, Ruditapes philippinarum, and the grooved carpet shell, R. decussatus, are within the top five species in terms of production volume and economic value. In this study we designed and validated the first medium-density 63K single nucleotide polymorphism (SNP) array for these two commercially important species. By leveraging a new chromosome-level genome assembly for R. philippinarum and that of R. decussatus, we identified over 300 million SNPs through whole-genome resequencing and genotyping-by-sequencing strategies. After stringent filtering, we selected 49,392 high-quality SNPs for R. philippinarum and 14,193 for R. decussatus to construct a dual-species array. Array validation was carried out by genotyping 384 individuals across multiple wild populations and hatchery samples, demonstrating excellent performance, with 67.7% and 67.5% of SNPs classified as high-quality polymorphic markers for R. philippinarum and R. decussatus, respectively. Minor allele frequency, missing data rate, and inter-marker distance met stringent quality thresholds, confirming the array robustness for clam population genetics. Parentage analysis in R. philippinarum families highlighted significant power for pedigree reconstruction in breeding programs. This publicly available genomic resource provides a reliable, cost-effective genotyping platform to enable population genomics and advanced selective breeding, genome-wide association studies, and genetic monitoring, ultimately strengthening management of genetic diversity and sustainable farming for two key clam species.

genomics↗

bioRxiv2025

Disentangling the role of chromosome inversions in the structure of flat oyster (Ostrea edulis): origin, adaptation and phylogeography

Chromosomal inversions are large-scale structural variants that disrupt recombination and contribute to population differentiation and local adaptation. In this study, we characterized the genomic features, frequency, and evolutionary significance of chromosomal inversions in the European flat oyster (Ostrea edulis), a species of ecological and commercial relevance. Using a low-density SNP array ([~]5K), we obtained confident genotyping data across the native European distribution of the species. The breakpoints of the inversions at chromosome (C) 2, C5 and C8, spanning 27, 7 and 35 Mb, respectively, were precisely mapped by combining linkage disequilibrium in a large sample and long-read sequencing. This enabled us to identify the SNPs and genes within the inversions for comparative population genomics and functional evaluation. A north to south cline was observed for the three inversions, although with low-moderate correlation between them. Strong signals for divergent selection were detected for the three inversions, although with specific profiles suggestive of adaptive peaks around highly divergent SNPs across the inversion length. The three inversions seem to be old considering genetic diversity and differentiation between arrangements. Phylogeographic events and adaptation to the current environment seem underlying the structural pattern observed. Gene content and enrichment analyses within inversions suggest that these polymorphisms may play a role in the immune system and response to different stressors including parasite resistance. Our results provide new insights into the genomic architecture of adaptation in O. edulis and highlight the potential of structural variants as targets for conservation and selective breeding.

genomics↗

bioRxiv2019

Potential of genomic selection for improvement of resistance to Ostreid Herpes virus in Pacific oyster (Crassostrea gigas)

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values (gEBVs) for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the \"summer mortality syndrome\". This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the Ostreid herpesvirus (OsHV-1-var). In the current study, we evaluated the potential of genomic selection for host resistance OsHV in Pacific oysters, and compared it to pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for seven days. 768 samples were genotyped using the medium density SNP array for oysters. GWAS was performed for the survival trait using a GBLUP approach in BLUPF90 software. Heritability ranged from 0.25{+/-}0.05 to 0.37{+/-}0.05 (mean{+/-}s.e) based on pedigree and genomic information, respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below [~]500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programs and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate gEBVs, thus potentially making the implementation of GS more cost effective.

genomics↗