SNPs are the most abundant polymorphism type,and have been explored in many crop genomic studies,including rice and maize.SNP discovery in allotetraploid cotton genomes has lagged behind that of other crops due to their complexity and polyploidy.In this study,genome-wide SNPs are detected systematically using next-generation sequencing and efficient SNP genotyping methods,and used to construct a linkage map and characterize the structural variations in polyploid cotton genomes.