The new red egg mutant Fuyin-lre was found in the germplasm resource preservation of silkworm (Bombyx mori) Fuyin.The new mutant is different from the previous red egg mutants of silkworm.Apart from the red color of the eggs,the mutant Fuyin-lre can result in embryonic lethality.The homozygous recessive embryos would cease developing after incubation for 4 to 5 days.In this study,whole-genome resequencing method was used to search for differential genes between Fuyin and Fuyin-lre based on the phenotype observation and genetic analysis of Fuyin-lre mutant.The result showed 660 differential genes with structural variation (SV),including 190 genes with frame-shift mutation.The expression of the red egg gene re and the genetic analysis showed that the embryonic lethal gene lre of the mutant Fuyin-lre is linked to the red egg gene re and is located on the 5th linkage group of silkworms.The resequencing result showed 34 genes with SV,including 12 genes with frame-shift mutations in the 5th linkage group between Fuyin and Fuyin-lre.The result significantly reduced the range of screening for lre gene and provided the basis for lre gene cloning.