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Background  High-throughput genotyping platforms play important roles in plant genomic studies. Cotton ( Gossypium  spp.) is the world’s important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world’s cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton.    Results  Here we report a high-throughput CottonSNP80K array and its utilization in genotyping detection in different cotton accessions. 82,259 SNP markers were selected from the re-sequencing data of 100 cotton cultivars and used to produce the array on the Illumina Infinium platform. 77,774 SNP loci (94.55%) were successfully synthesized on the array. Of them, 77,252 (99.33%) had call rates of >95% in 352 cotton accessions and 59,502 (76.51%) were polymorphic loci. Application tests using 22 cotton accessions with parent/F 1  combinations or with similar genetic backgrounds showed that CottonSNP80K array had high genotyping accuracy, good repeatability, and wide applicability. Phylogenetic analysis of 312 cotton cultivars and landraces with wide geographical distribution showed that they could be classified into ten groups, irrelevant of their origins. We found that the different landraces were clustered in different subgroups, indicating that these landraces were major contributors to the development of different breeding populations of modern  G. hirsutum  cultivars in China. We integrated a total of 54,588 SNPs (MAFs >0.05) associated with 10 salt stress traits into 288  G. hirsutum  accessions for genome-wide association studies (GWAS), and eight significant SNPs associated with three salt stress traits were detected.    Conclusions  We developed CottonSNP80K array with high polymorphism to distinguish upland cotton accessions. Diverse application tests indicated that the CottonSNP80K play important roles in germplasm genotyping, variety verification, functional genomics studies, and molecular breeding in cotton.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4062-2) contains supplementary material, which is available to authorized users.

High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis