Natsumi Sano, Shouji Houki, Nariaki Inoue
A decline in phytoplankton abundance caused by coastal oligotrophication has been suggested as a contributing factor to the decline of Manila clam (Ruditapes philippinarum) resources in Japan. The present study aimed to use gene expression analysis to evaluate the nutritional status of juvenile Manila clams. Juveniles were reared under nonfed and fed conditions, and three individuals were randomly sampled from each condition after 1, 3, 5, 10, 15, and 20 days. Total RNA was extracted from the whole body of each individual. Expression levels of 11 candidate genes were quantified by quantitative PCR to characterize gene expression profiles associated with nutritional status. These genes included five differentially expressed genes, three extracellular matrix (ECM)–related genes highlighted by an enrichment analysis identified in the previous RNA-seq study, and three enzyme-encoding genes previously reported in the Manila clam. Based on these expression data, a starvation probability model was developed to predict whether juveniles were starved or not. A generalized linear model assuming a binomial distribution with a logistic link function was applied, and model performance was evaluated using leave-one-out cross-validation. Variable selection based on the Akaike Information Criterion identified four genes—alpha-amylase, C-type lectin, defensin, and ECM-receptor interactions—as optimal predictors of individuals classified as starved, defined as fasting for 5 days or longer. The model was statistically significant and exhibited strong explanatory power. Moreover, it accurately predicted starved individuals with an accuracy of 81.6%. These results demonstrate the potential of gene expression-based modeling as a novel and practical tool for assessing the nutritional status of juvenile Manila clams and may contribute to elucidating causes of the decline in Manila clam resources and to advancing research aimed at its mitigation.