**5. Conclusions**

SSR markers can be used to describe the degree of differentiation between populations and to control the conservation of genetic resources. The study concludes that the evaluated cotton accessions have a broad genetic basis. The recurrent use of these accessions as parents will produce significant results. The genetic diversity and evolutionary relationship recognized among the uncharacterized genes and population structures established in this study would be informative to select parental accessions for breeding and genetic analysis as well as for efficient management and conservation of allotetraploid cotton genetic diversity. We identified DUF819 (PF005684), which is not only highly conserved but also plays an important role against biotic and abiotic stress, among four sequenced cotton species by using the WDR (PF00400) superfamily as reference genome-sequenced proteins. Additionally, the current diversity panel of semi-wild cottons will be invaluable as a community resource for measuring linkage disequilibrium (LD) and for fine-scale mapping of traits through LD mapping or a Genome-Wide Association Study (GWAS) that can be streamlined for genomics-assisted plant breeding programs. Our findings suggest that allotetraploid cotton species, including *G. barbadense* (AD2), *G. tomentosum* (AD3), *G. darwinii* (AD5), *G. ekmanianum* (AD6), and *G. stephensii* (AD7), are a rich source for the creation of genetic diversity in upland cotton.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/8/2401/ s1.

**Author Contributions:** K.W., A.D., and F.L. designed the experiments. A.D. and Z.Z. conceived the experiments and analyzed the results. A.D. and Z.Z. carried out the majority of the experiments and contributed equally. A.D. carried out all computational analyses. F.L., X.C., X.W., K.W.O., M.S., Y.X., Y.H., M.K.R.K., and M.S.I. participated in the mapping experiments. A.D. drafted the manuscript and K.W. revised the manuscript. All authors read and approved the final manuscript.

**Funding:** This research program was financially sponsored by the National key research and development plan (2016YFD0100306, 2016YFD0100203) and National Natural Science Foundation of China (31530053, 31671745).

**Acknowledgments:** We are indebted to give appreciation to State Key Laboratory of Cotton Biology, Institute of Cotton Research (ICR), Chinese Academy of Agricultural Sciences (CAAS); Anyang, China for providing umbrella for research program. We are also grateful to National Plant Germplasm System (NPGS), USA for providing germplasm. We express profound sense of reverence to Kunbo Wang and Fang Liu (Institute of Cotton Research), for timely guidance and provision of material whenever we needed during research work. To the entire research team, friends, and any other person who contributed, we have deep gratitude for you so much.

**Conflicts of Interest:** The authors declare no conflict of interest.
