Development and validation of the "Yucan-1" 5 K liquid chip for genomic studies in the silkworm (Bombyx mori)

The silkworm (Bombyx mori) is a lepidopteran model of paramount economic and scientific importance. While genomic resources are available, a high-throughput, cost-effective, and breed-specific genotyping platform for targeted genetic studies in Chinese local breeds, particularly those from Henan province, is still lacking. This study presents the development and validation of the "Yucan-1" 5 K liquid chip, a custom SNP array designed to empower genomic research in silkworms.

The chip was designed by integrating SNPs from three complementary sources: whole-genome resequencing data of 16 key Henan breeds (providing genome-wide coverage and diversity), FST analysis (capturing breed-differentiating loci), and pre-identified trait-associated and functional SNPs. The final array comprised 5,820 high-quality SNPs, achieving a genome-wide coverage of 98.99% with an average marker spacing of 79 kb. Extensive validation using 241 individuals demonstrated outstanding performance: a high genotyping call rate (> 99%), exceptional technical reproducibility (average concordance rate of 99.33%), and low genotyping error. Population genetic analyses (Principal Component Analysis, phylogenetic reconstruction, and ADMIXTURE) using the chip data effectively delineated the genetic structure of 12 Henan breeds, confirming its power to resolve fine-scale population stratification.An independent validation with 96 additional individuals from 10 breeds (including three external breeds) further confirmed the chip's high accuracy and generalizability for germplasm identification.

The "Yucan-1" chip is a robust, reliable, and highly efficient genotyping tool tailored for silkworm genomic research. t serves as a versatile platform for applications including germplasm characterization, population genetics, and breed authentication, thereby accelerating molecular breeding and conservation efforts for silkworms.