**5. Conclusions**

The purpose of cotton breeding is to boost and stabilize its yield in abiotic and biotic stress environments and to make cultivars with such physiological and architectural characteristics that can tolerate heat stress conditions. A low level of polymorphism is one of the major constraints for plant breeders and geneticists that can be attributed to the different processes like selection and domestication. It resulted in narrowing genetic shuffling in cotton. The use of an enormous number of SSRs can overcome the constraint of low polymorphism. In this study project, more than 1450 SSRs were assessed and the polymorphism rate was 12%, meaning the genetic diversity level was low owing to Intraspecific cross and segregation distortions. In spite of Intraspecific cross, 17 QTLs were detected by evaluating earlier-used and some novel traits. QTL detection can be attributed to a high rate of diversity in both parents. SSR markers were found best to deal with and easiest to assess polymorphism. The main goal of cotton breeding is to help increase and stabilize its productivity in stress environments and to develop cultivars with morphological traits which can withstand heat conditions. Our data suggest that favorable alleles for morphological traits can be combined to improve heat stress tolerance in cotton. Comparisons could be made to evaluate the consistency of QTL detection for the same trait in various backgrounds, which will help to determine the value of targeting these loci for selection in breeding programs.
