Rare variant analysis reveals divergent genetic architectures of directly selected and correlated silkworm traits

Abstract Correlational selection acts on combinations of correlated traits, driving multivariate phenotypic evolution, yet how it differentially shapes direct versus correlated traits remains unclear. Through rare variant association analysis of silkworm silk-yield traits, we reveal divergent genetic architectures of the direct traits cocoon shell weight (CSW) and ratio (CSR) versus the correlated traits cocoon and pupal weight (CW and PW). Direct targets were governed by fewer genes (11 and 12) enriched for deleterious, high-impact, negative-effect rare variants arising de novo during domestication and purged during improvement. Correlated traits involved more genes (25 and 65) with positive effects and moderate-impact variants largely inherited from wild silkworm, with frequency declines reflecting neutral processes. Selection signals confirmed stronger selection on CSW/CSR-associated genes. G-matrix analysis also revealed strong positive genetic correlations (rG: 0.336–0.814) during domestication, partly decoupled during improvement. Our study elucidates how artificial correlational selection altered historical correlations between these traits and shaped their distinct genetic architectures, providing empirical insights into correlational selection. Similar content being viewed by others Funding This work was supported by the National Natural Science Foundation of China (No. 32330102 to F.D., 32502989 to R.G., and 32472975 to C.L.), the National key research and development programme (Project No.2023YFD1600900 to X.T.), Natural Science Foundation of Chongqing, China (No. cstc2021jcyj-cxtt0005 to F.D.) and earmarked fund for China Agriculture Research System (no. CARS-17 to F.D. and X.T.). Author information Authors and Affiliations Corresponding author Ethics declarations Competing interests The authors declare no competing interests. Additional information Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Supplementary information Rights and permissions Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. About this article Cite this article Gao, R., Li, C., Hu, D. et al. Rare variant analysis reveals divergent genetic architectures of directly selected and correlated silkworm traits. Commun Biol (2026). https://doi.org/10.1038/s42003-026-10964-9 Received: Accepted: Published: DOI: https://doi.org/10.1038/s42003-026-10964-9