Deep learning empowers genomic selection of pest-resistant grapevine.

Journal: Horticulture research
Published Date: May 7, 2025

Abstract

Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study integrates deep learning (DL)/machine learning (ML) algorithms, plant phenomics, quantitative genetics, and transcriptomics to conduct genomic selection (GS) of pest resistance in grapevine. Building deep convolutional neural networks (DCNNs), we accurately assess pest damage on grape leaves, achieving 95.3% classification accuracy (VGG16) and a 0.94 correlation in regression analysis (DCNN-PDS). The pest damage was phenotyped as binary and continuous traits, and genome resequencing data from 231 grapevine accessions were combined in a Genome-Wide Association Studies, which maps 69 quantitative trait locus (QTLs) and 139 candidate genes involved in pest resistance pathways, including jasmonic acid, salicylic acid, and ethylene. Combining this with transcriptome data, we pinpoint specific pest-resistant genes such as and , which are crucial in herbivore responses. ML-based GS demonstrates a high accuracy (95.7%) and a strong correlation (0.90) in predicting pest resistance as binary and continuous traits in grapevine, respectively. In general, our study highlights the power of DL/ML in plant phenomics and GS, facilitating genomic breeding of pest-resistant grapevine.

Authors

  • Yu Gan
    Biomedical Engineering Department, Stevens Institute of Technology, Hoboken, NJ 07030 USA.
  • Zhenya Liu
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.
  • Fan Zhang
    Department of Anesthesiology, Bishan Hospital of Chongqing Medical University, Chongqing, China.
  • Qi Xu
    State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450052, China.
  • Xu Wang
    Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907.
  • Hui Xue
    Department of Radiology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
  • Xiangnian Su
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.
  • Wenqi Ma
    Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
  • Qiming Long
    National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Buxin Road, Dapeng New District, Shenzhen, 518000, China.
  • Anqi Ma
    National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Buxin Road, Dapeng New District, Shenzhen, 518000, China.
  • Guizhou Huang
    National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Buxin Road, Dapeng New District, Shenzhen, 518000, China.
  • Wenwen Liu
    School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, China.
  • Xiaodong Xu
    State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China.
  • Lei Sun
    1Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA.
  • Yingchun Zhang
    Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA; Guangdong Provincial Work Injury Rehabilitation Center, Guangzhou 510000, China.
  • Yuting Liu
    Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China.
  • Xinyue Fang
    National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Buxin Road, Dapeng New District, Shenzhen, 518000, China.
  • Chaochao Li
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.
  • Xuanwen Yang
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.
  • Pengcheng Wei
    Information Systems Technology and Design Pillar, Singapore University of Technology and Design, 485998, Singapore. Electronic address: pengcheng_wei@mymail.sutd.edu.sg.
  • Xiucai Fan
    National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China.
  • Chuan Zhang
    West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan Province 610000, China.
  • Pengpai Zhang
    School of Life Sciences, Henan University, Minglun Street, Kaifeng, 475004, China.
  • Chonghuai Liu
    National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China.
  • Lianzhu Zhou
    School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
  • Zhiwu Zhang
    Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA.
  • Yiwen Wang
  • Zhongjie Liu
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.
  • Yongfeng Zhou
    National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Longhua District, Haikou, 571101, China.

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