Whole-genome resequencing reveals the selection of adaptive evolution during the domestication of pearl oyster Pinctada maxima

Abstract

The aquatic environment has a major effect on the domestication of species for aquaculture in nearshore environments. Disruptions in the ion composition of marine ecosystems have a major effect on the growth and development of aquaculture populations. However, research on the adaptation of domesticated bivalves to nearshore environments and the potential underlying regulatory mechanisms is limited. Here, we collected domesticated offspring (F₁ and F₂) and wild individuals (F₀ and P_w) of Pinctada maxima from nearshore areas. We performed a comprehensive genomic data analysis using whole-genome resequencing data. This comprehensive analysis facilitated the identification of signatures of selection on key genes and yielded locus information associated with critical adaptive evolutionary (AE) events during the domestication process. We also evaluated genetic diversity metrics, including observed heterozygosity (H_o), expected heterozygosity (H_e), and the Fixation index (F_is). The findings indicated that domesticated P. maxima may experience balancing selection. In the second-generation domesticated stock, we identified 372 candidate selection regions and 624 genes. Local AE events in the domesticated offspring populations were confirmed via quantitative polymerase chain reaction. We proposed a potential compensatory mechanism in which calcium ions for the main effector genes calmodulin (PmCaM) and catabolite activator protein (PmCAP) are cyclically cached. Our findings enhance our understanding of the mechanisms underlying the regulation of calcium ions, which is essential for the adaptation of species to variation in environmental conditions.