**Acknowledgements**

We thank all faculties and graduate students in Cotton Research Institute, Nanjing Agricultural University and the other members of the cotton genomics and breeding communities for their contributions, and apologize for not citing many enlightening papers owing to space limita‐ tions. This study was supported by grants from 973 (2011CB109300), 863, Jiangsu Province Key Project (BE2012329), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.
