Cotton is the most important crop that growing all around the world due to its immense applications for the synthesis of agricultural based products, textile and branded products. Genome of cotton arises have been sequenced but some varieties are in process of completion of genome under the genome sequencing technology. The first sequence of the D-genome wild relative of cultivated cotton of G. raimondii has been sequenced that laid foundation the sequencing for other varieties. Cotton demand increased all around the world as compared to other fibers and polyester based fibers. Low or high temperature affected the crops rotation cycles. Soil and water has to be our number one limiting factor and our greatest challenge to improve the yield of all crops so that economy of agricultural farming can be improved. When cotton seeds are crushed by cotton then three distinct compounds are produced: oil, meal and hull that can be used in fertilizers to enrich agricultural soil. Diseases in cotton can be controlled under the splicing and modification through molecular techniques.