Text | China Science Daily reporter Wen Caifei's silkworm life cycle has rich phenotypic diversity. Is there a "dictionary" that allows genome map scientists to design silkworm breeding in a targeted manner according to their needs? Dai Fangyin's team (hereinafter referred to as

Category：science

2025-05-15

text | "China Science Daily" reporter Wen Caifei

The rich phenotypic diversity of silkworm life cycle. Photo provided by Silkworm Pangenome Project Team

Is there a "dictionary" that allows genome map scientists to design silkworm breeding in a targeted manner according to their needs?

000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 They completed the large-scale germplasm resource genome analysis ("Silkworm genome") in silkworms and drew the super pan-genome map of silkworms. This research is the first in the world to realize the digitalization of the silkworm gene bank and create a "digital silkworm", which plays a significant role in deepening functional genome research and promoting the modelization of silkworms and opening up silkworm design and breeding. Related research results were recently published online in Nature-Communication.

The largest long read long pan-genome

white and fat spring silkworm spit silk into cocoons. This magical little insect has witnessed the silk culture of our country for thousands of years.

Since the 1980s and 1990s, the performance of cocoon silk has not improved significantly, and the cultivation of new high-yield and ultra-high-yield varieties has fallen into a state of stagnation. The performance and survival ability of cultivated varieties are inconsistent, which seriously restricts the further improvement of the benefits of the sericulture industry.

The key to breaking the deadlock is breeding. Cultivating high-value silkworm varieties with high yield, high quality, high resistance and special properties is an important direction for silkworm breeding. The large-scale mining of excellent genes that control these traits has become the focus of the research on the genetics of silkworms and is also a difficult point.

"Because the reference genome of the silkworm before came from a single strain, the variation information can be provided is very limited, and it is difficult to support the large-scale and high-throughput mining of excellent breeding genes, which directly hindered the progress of silkworm molecular breeding work." Dai Fangyin said.

Tong Xiaoling, professor at the National Key Laboratory of Silkworm Genomic Biology, Southwest University, introduced that the research team sequenced 1,078 silkworm germplasm resources, including 47 wild mulberry silkworm , 205 silkworm local species, 194 practical species and 632 mutants. After sequencing the second and third generations of silkworms and wild mulberry silkworms, the research team drew a high-precision pan-genome map of silkworms, which included the most comprehensive genome information of silkworms and wild mulberry silkworms, and constructed the first high-resolution long-read pan-genome of silkworms.

It is worth mentioning that the silkworm pan genome released by the research team consists of 545 long reads and long sequenced samples. It is the largest long reads and long pan genome among animals and plants to date, and is called the silkworm super pan genome.

"Digital Silkworm" makes research efficient

Silkworm super pan-genome map covers all the genetic information of silkworms. Through this map, scientists can directly connect to the phenotype and genomic code. If the identification of genes or causal variations in specific traits in the past is like "looking for a needle in a haystack", it can now be said to be "catching a turtle in a jar" - the super pan-genome provides the "coordinate" guidance for "fine grid", which is like "looking for dictionaries" for experts.

This study completed genome sequencing of silkworm materials covering more than 90% of the world's representative germplasm resources of silkworms. These materials contain rich phenotypic diversity, including the yield and quality of different cocoon silk, resistance to disease and stress, body shape and color. "Acquiring complete genomic information of these extremely rich resources means building a 'Digital Silkworm Digital Gene Bank', realizing the digitization of the genetic information of the silkworm species - 'Digital Silkworm'." Dai Fangyin told " China Science Daily ".

He said that "digital silkworm" is similar to a silkworm genetic diversity dictionary, connecting phenotypes and sequences. By comparing the presence and missing genomes of a specific phenotype (comparative genome analysis), the genome sequences responsible for the relevant phenotype can be quickly and accurately found.

For example, before cloning a gene that controls important traits, it often requires resequencing the genome and comparing it with the reference genome, which takes 3 to 5 years.When genomic mutations in controlling traits are located in the regulatory region of the gene or some complex large fragment structural mutations, it is difficult to further study them.

Academician of the Chinese Academy of Engineering Xiang Zhonghuai told that using the silkworm super pan-genome map, scientific researchers will open a new chapter in the research on functional genomes of silkworms and molecular breeding.

For example, it can connect genotypes and phenotypes with high efficiency and high throughput, that is, fine analysis of the genetic basis of controlling traits; conduct research on the entire genome region, not limited to gene coding regions that account for less than 3% of the genome; study structural variations of large fragments in the genome, including gene duplication, large fragment insertion, deletion, inversion, as well as chromosome breakage, fusion, etc.

is expected to realize the "super silkworm" breeding plan

What important scientific discoveries will be made using the super pan-genome of silkworms for research?

Tong Xiaoling said that after domestication and improvement, its important economic traits include cocoon silk yield and quality, and the resistance to disease, stress resistance, docileness and crowding of silkworms have been greatly improved. However, due to the lack of understanding of the reasons for these traits, it is impossible to gather all excellent traits in the same silkworm variety.

research team identified 468 domestication-related genes and 198 improved-related genes, of which 264 and 185 newly identified domestication-related genes and improved-related genes were 264 and 185 respectively. At the same time, the research team clarified the genetic basis for the hybridization of Chinese practical species and Japanese practical species to produce the most prominent hybrid dominant species. These findings will promote the implementation of the "super silkworm" breeding program.

cocoon silk yield and quality (silk fineness, etc.) are important economic traits of silkworms, but the scientific research community still has unclear understanding of the key control genes for silkworm cocoon silk yield and quality. The super pan-genome can accurately and efficiently reveal the control genes of these two representative traits, providing direct targets for silkworm molecular breeding.

Not only that, the silkworm super pan-genome will also have an impact on the archaeological and biological worlds.

research team compared the genomic information of more than a thousand silkworms, and finally revealed that the silkworm originated from the middle and lower reaches of the Yellow River . This coincides with archaeological discoveries such as half of silkworm cocoon unearthed in Xia County, Shanxi Province, stone carvings of silkworm pupa , etc.

silkworms are rich in phenotypic diversity mutants, which is an ideal model biological for studying biodiversity . After long-term research by silkworm scientists from various countries, only more than 50 trait control genes have been identified so far, and most of the trait control genes are still unknown. Using the silkworm super pan-genome can easily determine the key genes and fine genomic mutation characteristics of insect alert color and embryonic diapause that are widely concerned.

It's no wonder a paper reviewer said excitedly: "This study reveals the complete pan-genome of silkworms, which will make silkworm researchers jump up with joy."