An overview is presented with regard to applications of visible and near infrared (Vis/NIR) spectroscopy, multispectral imaging and hyperspectral imaging techniques for quality attributes measurement and variety discrimination of various fruit species, i.e., apple, orange, kiwifruit, peach, grape, strawberry, grape, jujube, banana, mango and others. Some commonly utilized chemometrics including pretreatment methods, variable selection methods, discriminant methods and calibration methods are briefly introduced. The comprehensive review of applications, which concentrates primarily on Vis/NIR spectroscopy, are arranged according to fruit species. Most of the applications are focused on variety discrimination or the measurement of soluble solids content (SSC), acidity and firmness, but also some measurements involving dry matter, vitamin C, polyphenols and pigments have been reported. The feasibility of different spectral modes, i.e., reflectance, interactance and transmittance, are discussed. Optimal variable selection methods and calibration methods for measuring different attributes of different fruit species are addressed. Special attention is paid to sample preparation and the influence of the environment. Areas where further investigation is needed and problems concerning model robustness and model transfer are identified.

• Traits obtained by high-throughput phenotyping perform similarly or even better in GWAS than those obtained by traditional, manual methods. • Dynamic phenotyping contributing a lot for GWAS to identify time-specific loci. • High-throughput phenotyping, allowing noncontact and dynamic measurement, possesses great potential to provide high quality trait data for GWAS. • Future research should focus on the development of low-cost high-throughput phenotyping techniques and efficiency data/image analysis algorithm. • Research of using various high-throughput phenotyping techniques and GWAS on more diverse plant species and traits is urgently needed.

The feasibility of using hyperspectral imaging with convolutional neural network (CNN) to identify rice seed varieties was studied. Hyperspectral images of 4 rice seed varieties at two different spectral ranges (380–1030 nm and 874–1734 nm) were acquired. The spectral data at the ranges of 441–948 nm (Spectral range 1) and 975–1646 nm (Spectral range 2) were extracted. K nearest neighbors (KNN), support vector machine (SVM) and CNN models were built using different number of training samples (100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500 and 3000). KNN, SVM and CNN models in the Spectral range 2 performed slightly better than those in the Spectral range 1. The model performances improved with the increase in the number of training samples. The improvements were not significant when the number of training samples was large. CNN model performed better than the corresponding KNN and SVM models in most cases, which indicated the effectiveness of using CNN to analyze spectral data. The results of this study showed that CNN could be adopted in spectral data analysis with promising results. More varieties of rice need to be studied in future research to extend the use of CNNs in spectral data analysis.