面向我国重要农业生物育种产业发展重大需求，针对传统育种核心环节受制于经验的难题，围绕主要作物育种目标，以农业育种多组学大数据为基础，通过人工智能算法与育种大数据深度融合，主要开展智能算法和模型构建、智能设计育种等方面研究，为作物分子设计育种提供了核心技术支撑。实验室建立以来，研发了系列功能基因挖掘智能算法，揭示智能设计育种提供核心基因资源与关键育种元件；构建了复杂性状表型预测人工智能算法，形成智能设计育种的关键底层技术；研制高性能分子辅助育种平台与预测工具，支撑作物智能设计育种。相关研究成果在Molecular Plant, Advanced Science, Plant Biotechnology Journal等国际主流期刊发表SCI论文50余篇，授权发明专利12项、软件著作权15项，出版中英文专著各1部。
1. 代表性论文
(1) Kunhui He, Tingxi Yu, Shang Gao, Shoukun Chen, Liang Li, Xuecai Zhang, Changling Huang, Yunbi Xu, Jiankang Wang, Boddupalli M. Prasanna, Sarah Hearne, Xinhai Li, Huihui Li. Leveraging automated machine learning for environmental data‑driven genetic analysis and genomic prediction in Maize hybrids. Advanced Science (2025), 12(17):e2412423. DOI: 10.1002/advs.202412423
(2) Shoukun Chen, Hao Zhang, Shuqiang Gao, Kunhui He, Tingxi Yu, Shang Gao, Jiankang Wang, Huihui Li. Unveiling salt tolerance mechanisms in plants: integrating the KANMB machine learning model with metabolomic and transcriptomic analysis. Advanced Science (2025), 12(23):e2417560. DOI: 10.1002/advs.202417560
(3) Tingxi Yu, Hao Zhang, Shoukun Chen, Shang Gao, Ze Liu, Jiankang Wang, Jose Crossa, Osval A Montesinos‑López, Sarah Hearne, Huihui Li. EXGEP: a framework for predicting genotype‑by‑environment interactions using ensembles of explainable machine‑learning models. Briefings in Bioinformatics (2025), 26(4):bbaf414. DOI: 10.1093/bib/bbaf414
(4) Jingxin Wang, Liwei Liu, Kunhui He, Takele Weldu Gebrewahid, Shang Gao, Qingzhen Tian, Zhanyi Li, Yiqun Song, Yiliang Guo, Yanwei Li, Qinxin Cui, Luyan Zhang, Jiankang Wang, Changling Huang, Liang Li, Tingting Guo, Huihui Li. Accurate genomic prediction for grain yield and grain moisture content of maize hybrids using multi‑environment data. Journal of Integrative Plant Biology (2025), 67(5):1379–1394. DOI: 10.1111/jipb.13857
(5) Huihui Li, Luyan Zhang, Shang Gao, Jiankang Wang. Prediction by simulation in plant breeding. The Crop Journal (2025), 13(2):501–509. DOI: 10.1016/j.cj.2024.12.018
(6) Huihui Li, Xin Li, Peng Zhang, Yingwei Feng, Junri Mi, Shang Gao, Lele Sheng, Mohsin Ali, Zikun Yang, Liang Li, Wei Fang, Wensheng Wang, Qian Qian, Fei Gu, Wenbin Zhou. Smart Breeding Platform: a web‑based tool for high‑throughput population genetics, phenomics, and genomic selection. Molecular Plant (2024), 17(5):677–681. DOI: 10.1016/j.molp.2024.03.002
(7) Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li. Artificial intelligence in plant breeding. Trends in Genetics (2024), 40(10):891–908. DOI: 10.1016/j.tig.2024.07.001
(8) Shoukun Chen, Tingting Du, Zhangping Huang, Kunhui He, Maogeng Yang, Shang Gao, Tingxi Yu, Hao Zhang, Xiang Li, Shihua Chen, Chun-Ming Liu, Huihui Li. The Spartina alterniflora genome sequence provides insights into the salt tolerance mechanisms of exo-recretohalophytes. Plant Biotechnology Journal (2024), 22(9):2558-2574. DOI: 10.1111/pbi.14368
(9) Kelin Wang, Muhammad Ali Abid, Awais Rasheed, Jose Crossa, Sarah Hearne, Huihui Li. DNNGP, a deep neural network‑based method for genomic prediction using multiomics data in plants. Molecular Plant (2023), 16(1):279–293. DOI: 10.1016/j.molp.2022.11.004
(10) Maogeng Yang, Shoukun Chen, Zhangping Huang, Shang Gao, Tingxi Yu, Tingting Du, Hao Zhang, Xiang Li, Chun‑Ming Liu, Shihua Chen, Huihui Li. Deep learning‑enabled discovery and characterization of HKT genes in Spartina alterniflora. The Plant Journal (2023), 116(3):690–705. DOI: 10.1111/tpj.16397
2. 代表性专利、软著与专著
(1) "Genome-wide prediction method based on deep learning by using genome-wide data and bioinformatics features"， US012315600B2；
(2) 一种基于深度学习的功能基因预测方法，ZL202411676468.2；
(3) 一种基于机器学习的基因型和环境互作算法及其应用， ZL202410245774.4；
(4) 基于深度学习的全基因组预测方法，ZL202311218507.X；
(5) Linkage analysis and gene mapping, Jiankang Wang, Huihui Li, Luyan Zhang, Science Press and EDP Sciences, 2023.
3. 科技成果奖励
(1) 基于深度学习的全基因组预测方法DNNGP，2023年度海南省十大杰出农业科技成果，2024年。
