The deep neural network is used to establish a neural network model to solve the problems of low accuracy and poor accuracy of traditional algorithms in screening differentially expressed genes and function prediction during the walnut endocarp hardening stage. The paper walnut is used as the research object to analyze the biological information of paper walnut. The changes of lignin deposition during endocarp hardening from 50 days to 90 days are observed by microscope. Then, the Convolutional Neural Network (CNN) and Long and Short-term Memory (LSTM) network model are adopted to construct an expression gene screening and function prediction model. Then, the transcriptome and proteome sequencing and biological information of walnut endocarp samples at 50, 57, 78, and 90 days after flowering are analyzed and taken as the training data set of the CNN + LSTM model. The experimental results demonstrate that the endocarp of paper walnut began to harden at 57 days, and the endocarp tissue on the hardened inner side also began to stain. This indicates that the endocarp hardened laterally from outside to inside. The screening and prediction results show that the CNN + LSTM model’s highest accuracy can reach 0.9264. The Accuracy, Precision, Recall, and F1-score of the CNN + LSTM model are better than the traditional machine learning algorithm. Moreover, the Receiver Operating Curve (ROC) area enclosed by the CNN + LSTM model and coordinate axis is the largest, and the Area Under Curve (AUC) value is 0.9796. The comparison of ROC and AUC proves that the CNN + LSTM model is better than the traditional algorithm for screening differentially expressed genes and function prediction in the walnut endocarp hardening stage. Using deep learning to predict expressed genes’ function accurately can reduce the breeding cost and significantly improve the yield and quality of crops. This research provides scientific guidance for the scientific breeding of paper walnut.

Lignin de ciency in the endocarp of walnuts causes nuts exposed, lead a inconvenience in processing and transportation of walnuts, and easy to produce insect damage, mildew, affecting the quality of walnuts. Cinnamyl alcohol dehydrogenase (CAD) is the nal enzyme in the phenylpropanoid metabolic pathway in lignin, converting cinnamaldehyde to cinnamyl alcohol and catalyzing the synthesis of lignin monomers. To investigate the lignin metabolism pathway in walnut, the JrCAD genes were characterized. In this study, all 18 JrCADs were identi ed and phylogenetic relationships, gene structure, protein motifs, collinearity and expression pattern of the JrCADs were also analyzed. All JrCADs could be divided into three groups based on phylogenetic tree. Transcriptome data demonstrated that JrCADs have different expression patterns in walnut endocarp at development stages. Combined with qRT-PCR data, we nally identi ed several candidate JrCADs that involved in the process of endocarp sclerosis. These results provide valuable candidate genes for dissecting the functions and molecular mechanisms of lignin accumulation in walnut.

Lignin deficiency in the endocarp of walnuts causes nuts exposed, lead a inconvenience in processing and transportation of walnuts, and easy to produce insect damage, mildew, affecting the quality of walnuts. Cinnamyl alcohol dehydrogenase (CAD) is the final enzyme in the phenylpropanoid metabolic pathway in lignin, converting cinnamaldehyde to cinnamyl alcohol and catalyzing the synthesis of lignin monomers. To investigate the lignin metabolism pathway in walnut, the JrCAD genes were characterized. In this study, all 18 JrCADs were identified and phylogenetic relationships, gene structure, protein motifs, collinearity and expression pattern of the JrCADs were also analyzed. All JrCADs could be divided into three groups based on phylogenetic tree. Transcriptome data demonstrated that JrCADs have different expression patterns in walnut endocarp at development stages. Combined with qRT-PCR data, we finally identified several candidate JrCADs that involved in the process of endocarp sclerosis. These results provide valuable candidate genes for dissecting the functions and molecular mechanisms of lignin accumulation in walnut.

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