Abstract
Diapausing eggs are critical for rotifer population persistence and dispersal. Despite their ecological significance, the factors shaping their phenotypic variation and its genetic basis remain largely unexplored. We characterized morphological and biochemical traits related to dispersal in diapausing eggs of two cryptic rotifer species, Brachionus plicatilis and Brachionus rotundiformis, and examined the differences between floating and sinking eggs in B. plicatilis . Additionally, we performed a genome-wide association study in B. plicatilis to identify genetic variants associated with dispersal-related traits. Our analyses revealed pronounced interspecific variation: B. plicatilis produced larger and heavier diapausing eggs, while B. rotundiformis exhibited higher lipid content. Broad-sense heritability indicated stronger genetic control of most traits in B. plicatilis , whereas lipid area showed higher heritability in B. rotundiformis . Differences between floating and sinking eggs in B. plicatilis were linked to lipid content. Floating eggs displayed significantly higher lipid reserves. Genomic analyses identified SNPs significantly associated with embryo area, egg weight, and lipid content, located near genes involved in morphogenesis, embryo development, and a protein family involved in gap junction formation. This work represents one of the first GWAS applications targeting diapausing egg traits in aquatic microinvertebrates and provides insights into the genetic architecture governing dispersal strategies in rotifers.