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Ng Nanjing Agricultural University and its partners published papers to reveal the origin of all five allotetraploid cotton

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Where did cotton originate and how did it evolve? From being discovered to now, what are the mysteries of cotton genome? What innovations are needed for cotton breeding and improvement in the future? Recently, Nanjing Agricultural University, the University of Texas, Hassen alpha Institute of biotechnology, Texas A & M University and other units have cooperated to complete the mapping of high-precision reference genome of all five allotetraploid cotton species, providing an important reference for the exploration of polyploid plant genome evolution rules. The results were published online in the international authoritative academic journal Nature Genetics on the evening of April 20. (Title: genetic diversions of five Gossypium allopolyploid fields and their impact on Cotton Improvement)
It is understood that the main cultivated cotton is heterotetraploid, and its formation has undergone a complex process of hybridization, polyploidy and domestication. About 1.5 million years ago, diploid cotton originated in Africa and diploid cotton in Meizhou were crossed and genome doubled to form five heterotetraploid species, i.e. upland cotton, island cotton, wool cotton, brown cotton and Darwinian cotton. Among them, upland cotton and island cotton were domesticated into cultivated species, while wool cotton, brown cotton and Darwinian cotton were wild species. However, due to the complexity of quadruple genome itself and genome sequencing technology, the formation and evolution of these five species has not been accurately revealed.
In order to analyze the evolution of cotton and find out the excellent genes of wild cotton species, the high-precision reference gene set of all five allotetraploid cotton species was constructed by using the sequence of second and third generations (Illumina) and high-level chromatin structure capture (HIC) techniques. This latest study found that the formation of these five species is a single origin, and after 200000-600000 years of natural evolution, gradually formed five cotton species. Among them, upland cotton and island cotton have become the most important cultivated cotton after about 8000 years of independent artificial domestication. This means that, 8000 years ago, human ancestors living in different regions almost domesticated the two cotton species at the same time.
The evolution of cotton a the distribution of chromosome characteristics and interspecific genomic differences of cotton B
The study also found that the number and arrangement of genes did not change significantly in the process of hybridization, polyploidy and evolution of different cotton species in 1.5 million years. In the process of artificial domestication about 8000 years ago, the fiber length and quality of upland cotton and island cotton have changed significantly. The results showed that although upland cotton and island cotton were domesticated independently, domestication promoted the co expression network of fiber development genes to be consistent. This shows that even in two places, human ancestors coincidentally optimized similar gene expression patterns, which made the fiber length and color of the two cultivated cotton increased.
Generally speaking, the low gene recombination rate will affect the breeding efficiency. This study reveals that polyploidy can inhibit the genetic recombination rate by changing the level of epigenetic modification, which can be overcome by interspecific hybridization. In other words, interspecific hybridization can reactivate the gene recombination rate, and then improve the efficiency of cotton breeding.
It is understood that this achievement reveals the genetic and epigenetic laws of evolution and domestication of five polyploid cotton for the first time, and provides theoretical support and unique genome resources for improving cotton through interspecific hybridization, epigenetic breeding and gene editing. Professor Song Qingxin of Nanjing Agricultural University participated in the research as the co first author of the paper, and Dr. Ye Wenxue also participated in part of the work. The work of Nanjing Agricultural University was supported by the National Natural Science Foundation of China and Jiangsu Modern crop production collaborative innovation center.
Content source: Nanjing Agricultural University
Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.
Article link: https://www.nature.com/articles/s41588-020-0614-5
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