On April 13, 2020, Nature Genetics magazine published a major scientific research achievement, and through the assembly, optimization and comparative analysis of several cotton genomes, the Research Group of Zhu Yuxian of Wuhan University’s Institute of Advanced Studies and the Huada Gene Research Team resolved the dispute surrounding the origin of the cotton genome, and found a wealth of cotton agronomic character senome setype genetic sites and targets, which will accelerate the process of cotton genetic breeding improvement.
Cotton is one of the most important cash crops in the world, and its fiber, commonly known as leather cotton, is the main natural raw material of the textile industry. China is the world’s largest producer and consumer of textiles, is also a big cotton growing country, cotton fiber-related agronomic character improvement of the genetic target needs urgently, and the cultivation of cotton seed-related genomic research has thus become a hot research topic.
Using the latest sequencing and assembly techniques, the research team analyzed the world’s first high-precision weed genome (which is an African cotton variant with a genome type Of1) and upgraded the Asian cotton genome (A2) and land cotton genome (AD)1 to significantly improve the accuracy and completeness of the genome, providing a high-quality genomic resource for cotton-related agronomic studies.
Figure 1: The project assembles and optimizes the results of a presentation of key genomic parameters, in which the A1 genome is first deciphered.
There are 51 genus cotton plants, including 46 diples and 5 tetraploid cotton species. Hetero-tetramass land cotton (AADD) is the world’s highest yield, the most widely cultivated cotton species, its evolution and fiber development mechanism has been concerned. Studies have confirmed that the D subgenome donor of terrestrial cotton comes from Redmond cotton (DD). But the origin of the A subgenome donor has been controversial, with some scholars believing it is from Cotton Africa (A1) and others believing it to be from Asian cotton (A2).
By building the system to develop the tree and performing evolutionary analysis, the team found the true donor source of the A subgenome of terrestrial cotton: neither African cotton (A1) nor Asian cotton (A2), but the extinct, African cotton and Asian cotton common ancestor genome A0, and infer the time of differentiation between the A genome of terrestrial cotton, Cotton, and Asian cotton and the ancestral donor genome A0, thus ending the controversy over the origin of the terrestrial cotton subgenome.
Figure 2: Cotton A Genome Origin and Evolution Model (a) and Important Evolutionary Events (b).
In addition, the researchers also compared genomic analysis of different cultivated cotton species, identified a large number of structural variation sites, combined with different fiber development period gene difference symbiosis expression data, the impact of gene difference symbiosis expression of the mutation site screening, and finally through genetically modified verification experiments, to find the key genes of cotton fiber development. For example, when it was found that the differential gene was significantly enriched in the pathway associated with controlling the synthesis of ultra-long-chain fatty acids, the researchers selected the key gene in the pathway, KCS6, and used genetically modified experiments to over-express it, which confirmed that the fiber length of the terrestrial cotton was significantly improved under the over-expression regulation of the gene. The candidate sites identified by the research team by the above methods provide a wealth of genetic improvement sites and targets for cotton breeders, which will speed up the cotton breeding process.
Figure 3: Analysis of cotton genome structural variation and fiber development.
So far, the research team has provided high-quality genomic resources and genetic improvement evidence for the basic research and production practice of cotton by the evolution, comparative genomics and population genetic analysis of the three high-quality cotton genomes assembled, which will have an important role in promoting the breeding of cotton agronomic traits.
Extended Reading – Cotton Genome Memorabilia
African Cotton Genome (A1A1) Deciphered! The results were presented in Nature Genetics by the team of academicians Zhu Yuxian of Wuhan University’s Institute of Advanced Studies and the Huada Genetics Research Team through a variety of sequencing techniques, including Hi-C and PacBio. The team successfully assembled the genome of the cotton G.herbaceum (a variant of African cotton A1) and updated the Genomes of Asian Cotton (A2) and Terrestrial Cotton (AD)1).
The land cotton TM-1 and terrestrial cotton ZM24 genomes were presented by the Li Fuguang Research Team at Zhengzhou University’s School of Agriculture and the Huada Genetic Research Team in Nature Communications. For the first time, the research team revealed the effects of inverting the genetic diversity of land cotton and the differentiation of land cotton population.
The achievement of the AADD genome, published in collaboration with Nature Biotechnology, by the Cotton Research Institute of the Chinese Academy of Agricultural Sciences, huada Gene Research Team and Peking University, provides important insights into the evolution of the Terrestrial Cotton (TM-1) genome.
Cotton A (Asian cotton, tree cotton) genome, the results of the Chinese Academy of Agricultural Sciences Cotton Research Institute, Wuhan University Institute of Advanced Studies, Huada Genetic Research Team published in Nature Genetics. The team assembled a 1.7Gb genome using short-read long sequencing techniques and annotated 41,330 protein-coded genes. Repeat sequences accounted for 68.5%, the highest proportion of the then sequenced gemini plants.
The Redmond Cotton Genome (D) sketch was presented in Nature Genetics by the Cotton Research Institute of the Chinese Academy of Agricultural Sciences, the School of Life Sciences of Peking University, and the Huada Genetic Research Team. The researchers used short-read long sequencing techniques to assemble the 775Mb genome, and more than 73% of the sequences were anchored to 13 chromosomes. 40,976 protein-coded genes were obtained, 92% of which have functional annotations.