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Drought resistance (DR) is a complex trait that is regulated by a variety of genes. Without comprehensive profiling of DRrelated traits, the knowledge of the genetic architecture for DR in cotton remains limited. Thus, there is a need to bridge the gap between genomics and phenomics. In this study, an automatic phenotyping platform (APP) was systematically applied to examine 119 imagebased digital traits (itraits) during drought stress at the seedling stage, across a natural population of 200 representative upland cotton accessions. Some novel itraits, as well as some traditional itraits, were used to evaluate the DR in cotton. The phenomics data allowed us to identify 390 genetic loci by genomewide association study (GWAS) using 56 morphological and 63 texture itraits. DRrelated genes, including GhRD2, GhNAC4, GhHAT22 and GhDREB2, were identified as candidate genes by some digital traits …