Cotton genomics is providing rational ways for gene finding and genetic improvement

Cotton provides natural fiber resources for spinning, and is used by human beings for thousands of years. Traditional breeding methods contributed so much to cotton improvement, but breeders are not able to develop new variety with expectation. Cotton genomics, although complex as a tetraploid, developed so fast recently. The draft genomes for A, D, AD1 and AD2 are published in the recent years, which promoted GWAS analysis of cotton economic traits, with lots of genes identified. The evolution of genomes is described, many structural variations and gene mutations were identified, which will be very helpful for investigating interaction between genes and map-based cloning. We predict more and more genes will be cloned later on, which will be useful for molecular design breeding. Recently the 3D genome of cotton was studied, inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. The 3D genome study provides a new way in understanding genome structure and transcriptional regulation. The previous publications are surely advanced the knowledge of cotton genomics, but a reference-scale genome should be work out for more exactly designing a variety or molecular assisted breeding.