An Integrative Genome-Wide and Population-Based Analysis of Growth and Moltism Traits in a Core Strain Collection of the Silkworm (Bombyx mori)

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.