On the 3rd, the reporter learned from the Cotton Research Institute of the Chinese Academy of Agricultural Sciences that the team of researchers Li Fuguang and Yang Zhaoen has drawn an evolutionary roadmap for upland cotton, revealing the genetic mechanism of chromosome large segment variation regulating population genetic diversity and environmental adaptability, deciphering the genetic architecture of fiber quality traits, and opening up a new path for the creation of excellent cotton germplasm. The relevant results were published in the international academic journal Nature Genetics. Germplasm refers to the genetic material or material that transmits genetic information to offspring. Currently, regional centralized planting has brought challenges such as a sharp decline in genetic diversity and significant homogenization of cotton varieties. Exploring the molecular trajectory of upland cotton evolution, discovering outstanding genes in cotton germplasm that have not yet been bred and utilized, and creating new germplasm are important ways to solve the above problems. The research team utilized 107 representative germplasm samples of upland cotton to construct a super pan genome, which includes the total genome information of wild and cultivated upland cotton species; For the first time, a chromosomal translocation event of A03-A09 was discovered within upland cotton species, significantly affecting its population differentiation and regional adaptability. Further research has found that before the formation of cultivated upland cotton, wild upland cotton and semi wild upland cotton underwent three stages of structural variation. Using these structural variations as markers, upland cotton can be subdivided into 32 haplotypes. However, modern cultivated species only originate from one haplotype, with a narrow genetic basis. This study reveals the widespread presence of structural variations closely related to disease resistance in the pan genome of upland cotton. Among them, through the analysis of the NLR family of immune receptor coding genes against diseases, new sites for resistance to Verticillium wilt were identified, revealing the evolutionary pattern of the NLR gene family. At the same time, 69 loci related to fiber quality were identified through marker identification, of which 62 were previously undetected new loci. Multi effect genes regulating fiber strength and seed size were also discovered. The study also systematically mapped the genome-wide distribution of 127 large-scale inversions in upland cotton, revealing their key roles in important traits such as insect resistance and fiber color. For example, on chromosome A06, a 3.9Mb inversion significantly increases leaf epidermal density and is associated with insect resistance; On chromosome A07, the brown fiber phenotype determined by the Lc1 locus is controlled by two different inversion haplotypes. The above-mentioned functional inversions are closely linked to hundreds of genes within the region. Therefore, when selecting high insect resistance or ideal fiber color, a large number of non target trait genes may be inadvertently introduced, known as "linkage burden". This discovery reveals the potential cost of neutral trait improvement in traditional breeding and proposes a new breeding strategy of "breaking unfavorable chains and achieving precise editing". In this regard, Zhang Xianlong, an academician of the CAE Member and a professor of Huazhong Agricultural University, said that Li Fuguang and Yang Zhaoen's team screened 107 representative materials from more than 3600 germplasms, constructed the world's largest and most widely genetic diversity graphic pan genome map of upland cotton, revealed the evolution law of ribosomal DNA (rDNA) in the population for the first time, and provided a new scientific basis for clarifying the genetic diversity and phenotypic variation of upland cotton. The study also reconstructed the origin and diffusion patterns of upland cotton in the Americas, and found that large-scale structural variation is the core driving force for its environmental adaptability differentiation; The first panoramic map of the whole genome inversion of upland cotton has been drawn, providing a theoretical basis, precise targets, and design tools for efficient molecular design breeding. (New Society)