**2. Secondary metabolites in cotton**

As the name initially meant, plant secondary metabolites used to be considered as waste in metabolism without primary growth, development, and reproduction functions [10]. Nowadays, plant secondary metabolites usually refer to small molecules

*Utilization of Secondary Metabolites in Cotton Production DOI: http://dx.doi.org/10.5772/intechopen.114098*

produced in metabolism with ecological functions, such as defense and survival [10]. Plant secondary metabolites have a long history of being used as herbal medicine; their use in agriculture is a recent development. They are classified into terpenoids, phenolic compounds (flavonoids and phenylpropanoids), and N-containing compounds (cyanogenic glycosides, alkaloids, and glucosinolates) based on their biosynthetic pathways [11].

## **2.1 Cotton secondary metabolites**

Cotton secondary metabolites are flavonoids (including tannins), terpenoids, phenolic acids, and fatty acids. Alkaloids and sulfur-containing secondary metabolites have not been emphasized due to their number so far.

### *2.1.1 Flavanoids*

Flavonoids have a backbone diphenylpropane structure (C6-C3-C6) where two aromatic rings are linked *via* a three-carbon chain (**Figure 1**). The A ring is typically formed from a molecule of resorcinol or phloroglucinol synthesized *via* the acetate pathway with a characteristic hydroxylation pattern at positions 5 and 7 [12]. The B ring comes from the shikimate pathway with a characteristic hydroxylation pattern at positions 4<sup>0</sup> -, 3<sup>0</sup> , 4<sup>0</sup> -, or 3<sup>0</sup> , 4<sup>0</sup> , 5<sup>0</sup> -. One impressive phenomenon is that the number of characterized cotton flavonoids has significantly increased from 23 in 1994 [13] to 52 in 2017 [6], and up to 190 in 2023 [14]. With the MS/MS technique, it is easier to

**Figure 1.** *Typical flavonoid structures.*

identify more and more flavonoids, while the functions of the newly discovered flavonoids in cotton plants largely remain to be investigated. Of the reported ecological functions, signaling, defense, and coloring functions have been well studied as listed in **Table 1**.


*Utilization of Secondary Metabolites in Cotton Production DOI: http://dx.doi.org/10.5772/intechopen.114098*


