Quantitative trait locus (QTL) analysis is a powerful approach for identifying variants associated with the phenotypic variation of complex traits. However, selecting optimal methods and pre-processing steps require considerable time and effort. In this study, we demonstrated applicability and replicability of machine learning (ML) models in QTL analysis by evaluating their performance in comparison with conventional QTL analysis methods using 142 recombinant inbred lines derived from two japonica rice cultivars, Koshihikari and Baegilmi. Random forest and gradient boosting models showed the highest predictive accuracy, and consistently identified three QTLs associated with heading date: qDTH3, qDTH6, and qDTH7. Moreover, ML-based QTL analysis detected minor-effect qDTH10, where Koshihikari allele promoted heading date when combined with Koshihikari alleles of qDTH6 and qDTH7. These results demonstrate the applicability of ML models in QTL analysis on bi-parental mapping population in rice.

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Pathogens are the major causes of wheat crop yield losses, including the fungus Fusarium graminearum, an agent of Fusarium Head Blight (FHB). A better understanding of the relationship between plant morphological and biochemical traits and resistance to FHB can be effective in implementing a successful breeding program. This study investigated the relationship between FHB resistance as well as the morphological and biochemical traits in 20 durum wheat lines. Both morphological and biochemical traits were investigated using statistical tools. Therefore, analyses of variance, mean, as well as the correlation between the traits were con-sidered. In addition, for the morphological traits, cluster analyses were performed to identify similar genotypes in control and infected conditions. Furthermore, machine learning (ML) classification techniques, including Support Vector Machine (SVM), were proposed to detect the infected plants using morphological traits. The results show a great promise for the application of data-driven ML-based methods in plant breeding and disease detection.

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