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Credit: BGI Genomics

BGI Genomics, in collaboration with Southwestern University, the State Core Laboratory for Silkworm Genome Biology, and other partners, has created a high-resolution pangenome database representing nearly the entire genomic composition of the silkworm.

This research paper, which provides genetic insights into artificial selection (mating and breeding) and ecological adaptation, was published on September 24. Nature Connections.

Previously, there were not many sites associated with traits due to the scarcity of wild silkworms and the technical limitations of past studies. This is the first study to digitize the silkworm gene pool and create a ‘digital silkworm’, greatly facilitating functional genomics studies, promoting precision breeding and thereby enabling additional silk utilization.

The team deeply replicated the sequences of 1,078 silkworms (B. moriincluding 205 local strains, 194 improved varieties, 632 genetic stocks and 47 wild silkworms, B. mandarin) and assembled long-read genomes in 545 of these samples, generating 55.57 T of genomic data.

This pangenome database contains the most comprehensive information on domestic and wild silkworm genomes and is the largest long-read pangenome in the world for plants and animals to date. At the same time, in-depth research on various genetic variations, population structure, artificial selection and ecological adaptation and economic characteristics of silkworms has been conducted and fruitful results have been obtained.

Origin of the domestic silkworm

House silkworm, B. moridomesticated from the wild mulberry silkworm, B. mandarin. It has a history of more than 5,000 years, but the place of its domestication origin has long been an open question due to a lack of strong biological evidence.

The material in this study represents the richest genetic diversity of all the major sericulture regions of the world. The study found that endemic species in the lower and middle Yellow River region of China spread at the base of the house silkworm branch of the evolutionary tree, thus suggesting that the house silkworm originated in this region. Available archaeological evidence, including a half cocoon excavated in Xiyin Village, Xia County, Shanxi Province in 1926, and a stone-carved silkworm pupa excavated in 2019 in Shicun County, Shanxi Province, provide significant support for this conclusion.

Opening the bottleneck in sericulture

The traditional breeding of silkworms has a long and unique history, but has been at a standstill since the 1990s. Systematic analysis of the genetic basis of domestication and improvement of selection are essential to solve the outstanding problems in sericulture. The team identified 468 genes associated with domestication and 198 genes associated with improvement, of which 264 and 185 were newly identified, respectively. These genes will be important candidate targets for silkworm molecular improvement.

At the same time, it was found that Chinese and Japanese beneficial species shared less than 3% of the breeding sites. This not only reveals the relatively independent reproductive histories of the Chinese and Japanese silkworms, but also explains why this shared genetic base provides such hybrid advantages for both species. This result provides new ideas for future silkworm breeding.

Economic characteristics of sericulture

Silk yield and quality have long been considered as the main economic criteria for artificial selection of silkworms. However, to date, little is known about how genes and loci control these quantitative traits. The pangenome is arguably the “closest bridge” between phenotypes, especially complex traits.

An example is the regulation of silk production by a cell cycle-related transcription factor BmE2F1, which was revealed by selection signaling and structural variation. CRISPR-cas9-mediated knockout BmE2F1 it reduces the number of silk gland cells by 7.68% and silk productivity by 22%. Conversely, transgenic overexpression BmE2F1 increases the number of silk gland cells by 23% and silk productivity by 16%.

Fine silk has unique applications and higher economic value, but the genetic basis of fiber fineness was previously unknown. Analysis of rare variants in the genomes of cultivars led to their identification. BmChit β-GlcNAcase, a gene controlling silk fineness that is significantly detectable in fine species, and CRISPR-cas9-mediated knockout results in coarser silk fineness produced by native silkworms. This suggests that this gene plays a key role in determining silk fineness.

Adaptive features of sericulture

Diapause is a common ecological adaptation in insects that allows insects to survive despite adverse environmental conditions. Although the diapause hormone was first identified in the silkworm in 1957, little is known about the embryonic diapause gene. In this study, based on the analysis pnd silkworm strain and functional validation with genomic structural modification and gene editing, BmTret1-like gene has revealed itself as an important determinant of post-embryonic stagnation. This is the first time that a post-embryonic determinant gene has been identified in an insect.

This study reveals the complete pan-genome of the silkworm to reveal insights into artificial selection and ecological adaptation. “With a comprehensive sample and database combined with various experiments to identify genes for potential future research, we hope to accelerate the silkworm molecular design breeding process,” said co-author and BGI Genomics Senior Scientist Shuaishuai Tai.

About BGI Genomics

Headquartered in Shenzhen, China, BGI Genomics is a world-leading provider of genomic sequencing and proteomic services. BGI has topped the Asia Pacific and China life science corporate organization rankings for the seventh year running in the 2022 Nature Index Annual Rankings. Our services cover more than 100 countries and regions, covering more than 2,300 medical facilities.

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