Chemical and Structural Properties of Cotton Fiber Base and Associated Seed Coat

Trash content is one of the cotton fiber quality traits. Seed coat neps (SCNs) are among the most difficult-to-remove trash particles due to their strong attachment force with cotton fibers. The presence of SCNs is a major problem in the textile industry because SCNs create weak points in the yarn impact the dye uptake. Many environmental and management practices contribute to the generation of SCNs and recent studies reported that SCN count is cultivar dependent.  Cotton seed coats are composed of cellulose, hemicellulose, lignin, pectin, and wax substances. Understanding the amount and distribution of these macromolecules at the fiber base and associated seed coat will provide a new insight into their contributions to producing SCNs. We identified two cotton cultivars from a large number of F3 cotton lines with differences in CNs count. Then, we developed an integrated approach with Fourier transformed infrared (FTIR) spectroscopy and microspectroscopy imaging, microscopy techniques, and thermogravimetric analysis to characterize cotton fiber base and associated seed coats. These techniques altogether provide information regarding morphological, compositional, and biomolecules distribution in seed coats. In particular, FTIR microspectroscopy is widely used to identify biochemical composition and their relative distribution in highly complex biological tissues. FTIR images of 8 µm thick seed coat sections were analyzed using functional group distribution images and multivariate data analysis methods. We observed that these two cultivars show major differences in distribution of pectic acids or hemicellulose (vibrations 1734 and 1624 cm^-1) and lignin (vibration ~1504 cm^-1). K-mean clustering produced representative spectra for each layer of cotton seed coats, which were further compared to identify biochemical differences between cultivars. This study demonstrates that FTIR imaging could be used as a powerful non-destructive technique to investigate biochemical composition and distribution of biomolecules in seed coat sections.