Genomic selection serves as an effective way for crop genetic breeding, capable of significantly shortening the breeding cycle and improving the accuracy of breeding. Phenotype prediction can help identify genetic variants associated with specific phenotypes. This provides a data-driven selection criterion for genomic selection, making the selection process more efficient and targeted. Deep learning has become an important tool for phenotype prediction due to its abilities in automatic feature learning, nonlinear modeling, and high-dimensional data processing. Current deep learning models have improvements in various aspects, such as predictive performance and computation time, but they still have limitations in capturing the complex relationships between genotype and phenotype, indicating that there is still room for improvement in the accuracy of phenotype prediction. This study innovatively proposes a new method called DeepAT, which mainly includes an input layer, a data feature extraction layer, a feature relationship capture layer, and an output layer. This method can predict wheat yield based on genotype data and has innovations in the following four aspects: (1) The data feature extraction layer of DeepAT can extract representative feature vectors from high-dimensional SNP data. By introducing the ReLU activation function, it enhances the model’s ability to express nonlinear features and accelerates the model’s convergence speed; (2) DeepAT can handle high-dimensional and complex genotype data while retaining as much useful information as possible; (3) The feature relationship capture layer of DeepAT effectively captures the complex relationships between features from low-dimensional features through a self-attention mechanism; (4) Compared to traditional RNN structures, the model training process is more efficient and stable. Using a public wheat dataset from AGT, comparative experiments with three machine learning and six deep learning methods found that DeepAT exhibited better predictive performance than other methods, achieving a prediction accuracy of 99.98%, a mean squared error (MSE) of only 28.93 tones, and a Pearson correlation coefficient close to 1, with yield predicted values closely matching observed values. This method provides a new perspective for deep learning-assisted phenotype prediction and has great potential in smart breeding.

Accurate monitoring of rice-planting areas underpins food security and evidence-based farm management. Recent work has advanced along three complementary lines—multi-source data fusion (to mitigate cloud and spectral confusion), temporal feature extraction (to exploit phenology), and deep-network architecture optimization. However, even the best fusion- and time-series-based approaches still struggle to preserve fine spatial details in sub-meter scenes. Targeting this gap, we propose an HRNet-CA-enhanced DeepLabV3+ that retains the original model’s strengths while resolving its two key weaknesses: (i) detail loss caused by repeated down-sampling and feature-pyramid compression and (ii) boundary blurring due to insufficient multi-scale information fusion. The Xception backbone is replaced with a High-Resolution Network (HRNet) to maintain full-resolution feature streams through multi-resolution parallel convolutions and cross-scale interactions. A coordinate attention (CA) block is embedded in the decoder to strengthen spatially explicit context and sharpen class boundaries. The rice dataset consisted of 23,295 images (11,295 rice + 12,000 non-rice) via preprocessing and manual labeling and benchmarked the proposed model against classical segmentation networks. Our approach boosts boundary segmentation accuracy to 92.28% MIOU and raises texture-level discrimination to 95.93% F1, without extra inference latency. Although this study focuses on architecture optimization, the HRNet-CA backbone is readily compatible with future multi-source fusion and time-series modules, offering a unified path toward operational paddy mapping in fragmented sub-meter landscapes.