Genome-wide association study of economically important traits in the manila clam-Ruditapes Philippinarum

The Manila clam, Ruditapes philippinarum, is an economically important aquaculture species whose production is increasingly challenged by infection with the protistan parasite Perkinsus olseni. Developing sustainable strategies to control this disease is therefore essential for maintaining clam aquaculture. Selective breeding offers a potential approach to improve resistance to P. olseni while maintaining genetic diversity and adequate performance in commercially important traits, such as growth and shell characteristics. However, the successful implementation of breeding programmes requires an understanding of the genetic basis of these traits and the identification of genomic regions associated with variation in parasite burden and commercially relevant phenotypes. To address these objectives, we analysed dataset comprised 2,843 genotyped individuals, including 47 dams, 15 sires, and 2,781 offspring, with 16,331 SNPs retained after genotype quality control. The study combined genotype quality control, pedigree reconstruction, estimation of genetic parameters, genome-wide association studies (GWAS), and functional annotation to investigate the genetic architecture of infection, growth, and shell traits. Parentage assignment was performed using two complementary software packages, COLONY and Sequoia. Among the 2,176 offspring included in both analyses, the 724 offspring assigned to both parents by both methods showed complete agreement between COLONY and Sequoia, supporting the consistency of dual-parent assignments. However, Sequoia assigned at least one parent to 95.1% of offspring, compared with 62.3% using COLONY, thereby substantially reducing the proportion of offspring with no identified parent. Sequoia was therefore selected for downstream pedigree-based analyses because it provided a more complete and biologically coherent reconstruction of the experimental population. The reconstructed pedigree was subsequently used to quantify the genetic contribution to variation in growth, shell, and infection-related traits using Bayesian procedures. Bivariate animal models were fitted to the data; marginal posterior distributions of the (co)variance components and related parameters were estimated using Markov chain Monte Carlo (MCMC) methods implemented through a Gibbs sampler, as implemented in the module gibbsf90+ of the software BLUPF90+. Length, width, weight, height and thickness showed low-to-moderate heritability (h² = 0.175–0.348), whereas shell-colour traits showed moderate-to-very-high heritability (h² = 0.453–0.932). Several growth traits also showed negative genetic correlations with parasite burden, suggesting that genotypes associated with larger body size may tend to carry lower levels of P. olseni infection. GWAS and functional annotation further identified candidate genomic regions associated with parasite burden and shell-colour variation, including signals located on chromosomes 18 and 9. Overall, this study provides an integrated genomic framework for understanding the genetic basis of disease resistance and commercially relevant traits in R. philippinarum. The results demonstrate the value of parentage-informed genetic evaluation and identify candidate genomic regions that may contribute to variation in parasite burden and shell traits. Together, these findings provide a foundation for the future development of selective breeding strategies aimed at improving resistance to P. olseni while maintaining economically important characteristics and genetic diversity in Manila clam aquaculture. Further validation of the identified genomic associations will be required before their application in marker-assisted or genomic selection programmes. Keywords: Manila clam; Perkinsus olseni; disease resistance; heritability; genetic correlation; GWAS; functional annotation; selective breeding.