RESEARCH ARTICLE Open Access Development of chromosome-specific markers

with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific Lu et al. BMC Genomics (2015) 16:55 DOI 10.1186/s12864-015-1265-21State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaSSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available. (Continued on next page