Virescent mutant was first recognized from the upland cotton. Since its yellow-green phenotype was often found to be associated with the heterosis, this has been used as a phenotypic marker in cotton breeding. By taking use of three virescent mutants 71-7, 62-17 and 115-23, this work generated 33 hybridization combinations in order to genetically localize the underlying functional genes and to identify the elite lines with a potential used for cotton breeding. The genetic analysis suggested that a single recessive genetic locus causing virescent in sprout was present in mutants 71-7 and 115-23, respectively. A single locus with the incomplete dominant mode was detected in virescent mutant 62-17. We generated by backcross breeding approach with virescent marker, nine elite germplasms including male sterile lines, maintainer lines and restorer lines. Moreover, by analysis of comprehensive character of 12 dominant combinations, two lines Y34 and Y26 showed higher value on seed cotton yield and lint yield, and both can be used as new strains of precocious hybrid cotton in early maturing group of Xinjiang for Variety Screening Test. Taken together, this study provided new cotton germplasm resource, which might be used in identification of the functional genes and breeding of elite upland cotton varieties in Xinjiang.