**4. Conclusions**

Cotton plants are rich in secondary metabolites, which mainly include terpenoids, flavonoids, and phenolic acids. Terpenoids are not soluble in water, stored in pigment glands, including monoterpenes, sesquiterpenoids, and heliocides. They can deter insects and pathogens. One representative is gossypol, whose main sources are cotyledons and living roots. Cotton root gossypol concentration is a cumulative index for cotton plant stresses and defense response, and potentially used as a stress assessment tool for cotton crop management. It also increases with cotton plant age and size, reaching around 1% root fresh weight at harvesting stage and representing a heavier dose than other herbicides and insecticides. The impact of the high-dose gossypol in cotton roots after harvest on soil health and cotton plants next season is expected to be confirmed in the near future. Flavonoids used to be thought only as pigments but recent literature showed they can also deter insects and pathogens. A key difference of flavonoids from terpenoids is that they are soluble in water and stored in vacuoles. The allelopathic properties of flavonoids are expected to be confirmed in the near future. Tannins are a special group of flavonoids as they can bond to and precipitate protein and are also involved in deterring insects and pathogens. Phenolic acids are often precursors in flavonoids synthesis and soluble in water. Literature shows they are active to deter insects and pathogen and also allelopathic to suppress weeds.

Traditionally, all the three classes of cotton secondary metabolites terpenoids (gossypol), flavonoids, including tannins and phenolic acids, are integrated in cotton screening and breeding programs. Recent progresses have expanded their application in cotton production; direct extraction of the secondary metabolites and application; use of chemical regulators or elicitors of cotton secondary metabolites to change their concentrations *in situ* to achieve the functions of the target secondary metabolites, and change of the genetic bases of the secondary metabolites to produce or not to produce one or a set of secondary metabolites in crop plants *in situ* to achieve some benefits, which include reduction of the toxic gossypol in cotton seeds to increase their value in utilizing their oil and protein.
