The present disclosure is in the field of plant breeding. The disclosure provides methods for breeding cotton plants having a staygreen trait using marker-assisted selection. The disclosure further provides germplasm that stays green under high drought stress and provide yield advantage over non-staygreen germplasm. The disclosure also provides genetic markers associated with staygreen QTLs for introgressing these QTLs into elite germplasm in a breeding program and producing novel cotton germplasm that performs better under water-limited conditions.