Understanding the genetic basis of growth and moltism in silkworm (Bombyx mori) is essential for improving silk production efficiency and elucidating the mechanisms underlying developmental plasticity. Thus, this study aimed to establish a collection of 20 representative B. mori core strains and perform integrative genomic analyses combining genome-wide association studies (GWASs) and population-specific variant detection. A total of 5,293,831 high-confidence single-nucleotide variants (SNVs) were identified across the population, and GWAS revealed significant associations between specific genetic loci and four growth-related traits: larval weight at day 7 of the fifth instar, pupal weight, cocoon weight, and cocoon layer weight. Among these, two missense variants within the Cycb gene were significantly correlated with increased body weight at the late fifth instar stage, suggesting a potential role for this isoform in regulating cell-cycle-driven tissue expansion during rapid larval growth. Moreover, a population-based comparison identified 2803 trimolter-specific missense SNVs in 1440 genes, of which 109 were functionally annotated. Notably, homozygous variants were detected in key developmental regulators, such as MET1 and TOR1, implying potential alterations in juvenile hormone signaling and nutrient-dependent growth pathways that may contribute to the dominant trimolter phenotype. Although experimental validation remains necessary, these findings provide a genomic framework for understanding the molecular mechanisms underlying moltism variation and offer valuable resources for future silkworm genetic improvement.

Bombyx mori is a key insect in the sericulture industry and one of the very important economic animals that are responsible for not only the livelihood of many farmers internationally but also expended biomedical use. The National Institute of Agricultural Sciences of the Rural Development Administration of Korea (NIAS, RDA, Korea) has been collecting silkworm resources with various phenotypic traits from the 1960s and established breeding lines for using them as genetic resources. And these breeding line strains have been used to develop suitable F1 hybrid strains for specific use. In this study, we report the whole-genome sequences of 37 breeding line B. mori strains established over the past 60 years, along with the description of their phenotypic characteristics with photos of developmental stages. In addition, we report the example phenotypic characteristics of the F1-hybrid strain using these breeding line strains. We hope this data will be used as valuable resources to the related research community for studying B. mori and similar other insects.