From root to result: Portable NIRS-based non-destructive prediction of cassava quality traits

Abstract

Cassava (Manihot esculenta Crantz) is a staple food and a key industrial crop across tropical regions, but traditional phenotyping for critical quality traits like dry matter content (DMC) and starch content (StC) is a laborious and low-throughput process. This study investigates the efficacy of a handheld near-infrared spectrometer device (NIRS) for the non-destructive, rapid prediction of these traits. The research methodology involved collecting spectral data from 2,236 cassava clones from 19 field trials in Brazil, using two sample types: fresh roots and mashed roots. Six spectral pre-processing methods and three machine learning algorithms—Partial Least Squares (PLS), Support Vector Machines (SVM), and Extreme Gradient Boosting (XGB)—were evaluated to optimize predictive models. Model performance was assessed using the coefficient of determination in calibration (RC), the root mean squared error of calibration (RMSEC), and the Kappa index to quantify the consistency of clone selection. Results show that mashed samples consistently yielded superior predictive performance across all models. Specific preprocessing methods, such as Savitzky-Golay filtering combined with Standard Normal Variate (SG + SNV) and first-derivative transformations, significantly enhanced model accuracy. Among the algorithms, PLS demonstrated the best overall performance, with high predictive accuracy (RC >0.96) and low prediction errors (RMSEC<1.3 for DMCo), especially with mashed samples. High Kappa index values, consistently approaching 1.0, confirmed a good alignment between NIRS-based selection and traditional phenotypic methods. This study validates a portable spectrometer as a reliable and efficient tool for high-throughput phenotyping in cassava breeding programs. The findings confirm that portable NIRS devices, when used with optimal sample preparation (mashed roots) and robust modeling (PLS), can effectively yield good predictions for plant selection. This approach can significantly accelerate breeding cycles by enabling rapid, early-stage selection decisions, thereby overcoming a major bottleneck and contributing to a more efficient and sustainable genetic improvement of cassava.