Attenuated total reflection FT-IR spectroscopy with soft independent modeling of class analogy/principal component analysis for classifying cotton fiber maturity phenotypes of cotton population composed of various genotypes

Authors: Liu, Yongliang; Kim, Hee-Jin

Submitted to: Applied Spectroscopy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/16/2023
Publication Date: 11/7/2023
Citation: Liu, Y., Kim, H.J. 2023. Attenuated total reflection FT-IR spectroscopy with soft independent modeling of class analogy/principal component analysis for classifying cotton fiber maturity phenotypes of cotton population composed of various genotypes. Applied Spectroscopy. https://doi.org/10.1177/00037028231211942.
DOI: https://doi.org/10.1177/00037028231211942

Interpretive Summary: Rapid and accurate identification of fiber maturity phenotypes and genotypes is of importance to breeders. Either conventional fiber measurements (i.e., micronaire and lint percentage) or attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopic analyses has been used to discriminate immature fiber (im) phenotype from wild type (WT) mature fiber phenotype in a segregating F2 population, but these methods could not exhibit the minor phenotypic differences among the WT fibers composed of two different genotypes, WT homozygosity (WT-homo) and WT heterozygosity (WT-hetero). This research explored FT-IR technique, in combination with soft independent modeling of class analogy of principal component analysis (SIMCA/PCA), for the discrimination of WT fiber phenotypes consisting of two fiber genotypes (WT-homo and WT-hetero). There was a successful classification between WT-hetero fibers and WT-homo fibers. The results could provide cotton breeders and geneticists a sensitive and rapid tool for monitoring subtle differences within the WT fibers and further for dissecting genotype-phenotype interactions of cotton fibers.

Technical Abstract: Maturity is a major fiber trait that affects the processing and performance of cotton fiber. Rapid and accurate identification of fiber maturity phenotypes and genotypes is of importance to breeders. Previous studies showed that either conventional fiber measurements or attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopic analysis discriminated the immature fiber (im) phenotype from the wild type (WT) mature fiber phenotype in a segregating F2 population from a cross between two upland cotton lines differing in fiber maturity. However, both conventional fiber property measurement methods and FT-IR analyses with current algorithms could not detect the subtle differences among the WT fibers composed of two different genotypes, WT homozygosity (WT-homo) and WT heterozygosity (WT-hetero). This research explored FT-IR method, in combination with soft independent modeling of class analogy of principal component analysis (SIMCA/PCA), for the discrimination of WT fiber phenotypes consisting of two different genotypes (WT-homo and WT-hetero). The new approach enabled detecting IR spectral intensity differences between WT-homo and WT-hetero fibers. Successful classification originated from a distinctive spectral difference in low-wavenumber region (< 700 cm-1) between WT-hetero fibers and WT-homo fibers. This observation emphasized that ATR FT-IR spectroscopy with an SIMCA/PCA approach would be a sensitive tool for classifying the WT fibers demonstrating minor phenotypic differences. The improved sensitivity of the IR method may provide a way of dissecting genotype-phenotype interactions of cotton fibers rapidly and efficiently.