Objective  Genes related to the cocoon shell ratio of Bombyx mori were investigated for improvement on silkworm productivity.

  Method  Segregated BC₁ populations of a highly productive silkworm, Jingsong, and a moderately productive Furong were established. DNA pools were constructed by mixing 30 high and low cocoon shell ratio individuals from the BC₁ male populations. BSA-seq was applied to identify the regions relevant to the target trait. The coding genes at the candidate regions were annotated with BLAST software in GO and KEGG databases.

  Result   The percentage of clean reads that matched the reference genome of P50 was 98.86%, and those of the average genome coverage 95.79% for 1× and 88.63% for 5×. Variant calling resulted in 26 557 646 SNPs. Three QTLs for the cocoon shell ratio detected by ∆(SNP-index) were in the intervals of 4 430–4930 kb on Chr.2, 12350–12920 kb on Chr.4, and 3230–3730 kb on Chr.13. There were 70 coding genes found in the associated regions. According to the GO database annotation, 58 genes were categorized in the groups of biological process, molecular function, or cellular component. The 19 genes annotated in the KEGG database distributed in 34 metabolic pathways. Of which, 10 might play important roles in regulating the cocoon shell ratio and the functions involving the silk gland cell movement, energy metabolism, and/or protein synthesis.

  Conclusion   The genes related to the silkworm cocoon shell ratio were identified by BSA-seq method. Ten genes were speculated to possibly associate with the silk formation. The present study only managed to locate the regions on chromosomes 2, 4, and 13 of the genes in B. mori that might related to the cocoon shell ratio. Further study will be needed to finely map and clone the key regulatory genes in the highly complex regulatory mechanism.