Recessive embryonic lethal mutations uncovered in heterozygous condition in silkworm semiconsomic strains

In this study, we found two embryonic lethal mutations, t04 lethal (l-t04) and m04 lethal (l-m04), in semiconsomic strains T04 and M04, respectively. In these semiconsomic strains, the entire diploid genome, except for one chromosome 4 of the wild silkworm Bombyx mandarina, is substituted with chromosomes of the domesticated silkworm B. mori, and l-t04 and l-m04 mutations are located on B. mandarina-derived chromosome 4. To clarify the cause of the lethalities and the genes responsible for these mutations, positional cloning and CRISPR/Cas9 mediated knockout screening were performed. Finally, genetic complementation tests identified the mutations responsible for the l-t04 and l-m04 as the Bombyx homolog of imaginal discs arrested (Bmida) and TATA box binding protein-associated factor 5 (BmTaf5), respectively. Lethal stages of each knockout mutant indicated the importance of these genes in B. mori late embryogenesis. The lethal mutations responsible for l-t04 and l-m04 were not found in parental strains or wild B. mandarina collected from 39 distinct locations in Japan, indicating that both mutations were independently introduced during or after the development of the semiconsomic strains. We conclude that the recessive embryonic lethality in the T04 and M04 strains is due to deleterious mutations produced in B. mandarina-derived chromosome 4. [Display omitted] •Embryonic lethal mutations l-t04 and l-m04 were found in semiconsomic strains of Bombyx mori and B. mandarina.•Positional cloning and CRISPR/Cas9-mediated knockout identified genes responsible for mutations l-t04 and l-m04.•B. mori genes responsible for mutations l-t04 and l-m04 are orthologs of ida and Taf5, respectively.•Mutations l-t04 and l-m04 were not found in parental or wild B. mandarina strains.•Absence of l-t04 and l-m04 in parental strains indicates they have arisen during/after semiconsomic strain development.