Scientists have mapped the silkworm super pan-genome

Rich phenotypic diversity at all stages of the silkworm life cycle Courtesy of the Silkworm Pangenome Project Group

Structural variation characteristics of 545 silkworm genomes Courtesy of the Silkworm Pangenome Project Group

Is there a “dictionary” that allows genome mapping scientists to design silkworm breeding on a targeted basis?

Dai Fangyin, director of the State Key Laboratory of Silkworm Genomic Biology (hereinafter referred to as the “research team”), turned this dream into a reality. They completed the genome analysis of large-scale silkworm germplasm resources (“thousand silkworm genomes”) and drew a super pan-genome map of silkworms. This research is the first in the world to realize the digitization of silkworm gene bank and create a “digital silkworm”, which has a major role in deepening the study of functional genomes and promoting the pattern of silkworms, and opening up silkworm design breeding.

The relevant research results are entitled “High-resolution silkworm pan-genome analysis of artificial selection and genetic basis of ecological adaptation traits”, which has been published online in Nature – Communication.

The largest long-reading long pan-genome

The white and fat spring silkworm, squirming body spitting silk as a cocoon, this scene year after year, witnessing thousands of years of silk culture in China.

In 1914, Japan began to fully promote a generation of silkworm hybrids. Due to the early start, the key economic traits of silkworms, especially the production of cocoon silk, have also entered the improved platform period early. Since the 1980s and 1990s, the correlation performance of cocoon silk has not been significantly improved, and the breeding of high-yielding and ultra-high-yield new varieties has stagnated, or it is not coordinated with its viability, which has seriously limited the further improvement of the efficiency of the sericulture industry.

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

“Because the previous silkworm reference genome comes from a single strain, the variation information that 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 limits the promotion of silkworm molecular breeding.” Dai Fangyin said.

According to Tong Xiaoling, a professor at the State Key Laboratory of Silkworm Genomic Biology at Southwest University, the research team sequenced 1,078 silkworm germplasm resources, including 47 wild silkworms, 205 silkworm species, 194 practical species and 632 mutants. After the second and third generations of sequencing of silkworms and wild silkworms, a high-precision pan-genome map of silkworms was drawn, which included the most comprehensive genomic information of silkworms and wild silkworms, and constructed the first high-resolution long-reading long pan-genome of silkworms.

It is worth mentioning that the silkworm pangenome published by the research group is composed of 545 samples of long-reading long-reading long-sequencing, which is the largest long-reading long-read pan-genome in animals and plants so far, known as the silkworm super pan-genome.

“Digital silkworms” make research efficient

The silkworm super pan-genome map covers all the genetic information of silkworms, through which scientists can directly dock phenotypes and genomic codes. If the identification of genes or their causal variants of a particular trait used to be like “finding a needle in a haystack”, it can now be described as “catching a turtle in an urn” – the super pangenome provides “coordinates” guidance for “fine gridding”, which is like a “dictionary” for experts.

The silkworm materials that completed genome sequencing covered more than 90% of the representative germplasm resources of silkworms in the world, and these materials were rich in phenotypic diversity, including different cocoon silk yield quality, growth and development, disease resistance and stress resistance, body size and body color. “Obtaining the complete genomic information of these extremely rich resources also means building a ‘digital gene bank of silkworms’ and realizing the digitization of the genetic information of this species – ‘digital silkworms’.” Dai Fangyin told China Science News.

He said that “digital silkworm” is similar to a dictionary of silkworm genetic diversity, connecting phenotypes and sequences. By comparing the genomes of specific phenotypes (comparative genomic analysis), the genomic sequence responsible for the phenotype can be found quickly and precisely.

Before cloning a gene that controls an important trait, it often takes 3 to 5 years to resequence it through genome resequencing and comparing it with the reference genome. When the genomic variants that control traits are located in the regulatory region of genes or some complex large-fragment structural variations, it is difficult to study them further.

Using the silkworm super pan-genome atlas, it is possible to connect genotypes and phenotypes with high efficiency and high throughput, that is, to finely analyze the genetic basis of controlling traits; Conduct research on genome-wide regions, not just the coding regions of genes that make up less than 2% of the genome; Large-fragment structural variation in the genome is studied, including gene duplication, large-fragment insertion, deletion, inversion, chromosomal rupture, fusion, etc.

Xiang Zhonghuai, an academician of the Chinese Academy of Engineering, said that using the silkworm super pan-genome map, researchers will open a new chapter in the study of the functional genome of silkworms and the study of molecular breeding.

It is expected to promote the realization of the “super silkworm” breeding program

What are the important scientific discoveries using the silkworm super pan-genome?

Tong Xiaoling said that after the domestication and improvement of silkworms, their important economic traits include silk yield, quality, silkworm disease resistance, mildness and congestion resistance and other traits have been greatly improved, but due to the lack of understanding of the causes of these traits, it is impossible to gather all excellent traits in the same silkworm variety.

The research team identified 468 domestication-related genes and 198 improved-related genes, of which 264 and 185 were newly identified. At the same time, the genetic basis for the most prominent hybrid dominant species produced by the crossbreeding of Chinese practical seeds and Japanese practical seeds is elucidated, and these findings will promote the realization of the “super silkworm” breeding program.

Cocoon silk yield and quality (silk scale, etc.) are important economic traits of silkworms, but the current scientific research community is still unaware of the key control genes for silkworm cocoon silk yield and quality. The application of the super pangenome can accurately and efficiently reveal the control genes of these two representative traits, providing a direct target for silkworm molecular breeding.

Not only that, the silkworm super pangenome also affects the archaeological and biological worlds.

The research team compared the genomic information of more than 1,000 silkworms, and finally revealed that silkworms originated in the middle and lower reaches of the Yellow River. This coincides with archaeological discoveries (such as half a silkworm cocoon unearthed in Xia County, Shanxi, stone carved silkworm pupa, etc.).

Silkworms are rich in phenotypic diversity mutants, is an ideal model organism for the study of biodiversity, after long-term unremitting research by sericulturers in various countries, only more than 50 trait control genes have been identified, and the control genes of most traits are still unknown. The application of silkworm super pan-genome can easily determine the key genes and fine genomic mutation characteristics of the widely concerned insect alert color and embryonic diapause.

It’s no wonder that one reviewer excitedly said, “The study reveals the complete pangenome of silkworms, which will make silkworm researchers open their eyes and jump with joy.” (Source: China Science Daily, Wen Caifei)

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