Use of ATR FT-IR Spectroscopy in Classifying Different Degree of Fiber Secondary Cell Wall Developments between Immature Fiber (im) Mutant and Texas Marker-1 (TM-1) Cotton Fibers

The immature fiber (im) mutant is an upland cotton mutant with unique characteristics of non-fluffy cotton bolls. Compared to its wild type near-isogenic line (NIL) Texas Marker-1 (TM-1), im fiber consists of a thinner and less mature secondary cell wall. In this study, we applied three previously proposed simple algorithms for determining infrared maturity (M_IR), crystallinity (CI_IR), and R Value, along with principal component analysis (PCA), to analyze the attenuated total reflection Fourier transform infrared (ATR FT-IR) spectra for potential differentiation of developing and developed cotton NIL fibers. Unlike the first principal component (PC1) score and the R Values that enabled classification of different developmental stages of NIL fibers, a single use of M_IR or CI_IR index could not distinguish developed fibers from developing fibers well. However, a combination of M_IR and CI_IR value offered significant difference in fiber M_IR and CI_IR development between developing and developed fibers as well as within TM-1 fibers or im fibers. Since ATR FT-IR method enables the measurement of fiber maturity and crystallinity properties on small amount of breeder’s fiber samples in a rapid and non-destructive way, it provides an alternative tool of phenotyping cotton fibers and can help geneticists and breeders interpret their genetic and genomic data.