数字农科院2.0

Fast-forwarding plant breeding with deep learning-based genomic prediction

文献类型: 外文期刊

作者: Gao; Shang;Yu; Tingxi;Rasheed; Awais;Wang; Jiankang;Crossa; Jose;Hearne; Sarah;Li; Huihui

作者机构:

关键词: artificial intelligence;deep learning;genomic prediction;plant breeding

期刊名称: JOURNAL OF INTEGRATIVE PLANT BIOLOGY

ISSN: 1672-9072

年卷期: 2025 年

页码:

收录情况: SCIE(2025版) ; ; CSCD(2025-2026年度) ; ; 科技核心(2024版)

摘要: Deep learning-based genomic prediction (DL-based GP) has shown promising performance compared to traditional GP methods in plant breeding, particularly in handling large, complex multi-omics data sets. However, the effective development and widespread adoption of DL-based GP still face substantial challenges, including the need for large, high-quality data sets, inconsistencies in performance benchmarking, and the integration of environmental factors. Here, we summarize the key obstacles impeding the development of DL-based GP models and propose future developing directions, such as modular approaches, data augmentation, and advanced attention mechanisms.

分类号:

  • 相关文献

[1]A review of multimodal deep learning methods for genomic-enabled prediction in plant breeding. Montesinos-Lopez, Osval A.,Chavira-Flores, Moises,Kiasmiantini, Leo,Crespo-Herrera, Leo,Saint Piere, Carolina,Li, Huihui,Fritsche-Neto, Roberto,Al-Nowibet, Khalid,Montesinos-Lopez, Abelardo,Crossa, Jose. 2024

[2]Dairy farming in the era of artificial intelligence: trend or a real game changer?. Oscar R. Espinoza-Sandoval,Juan Carlos Angeles-Hernandez,Manuel Gonzalez-Ronquillo,Navid Ghavipanje,Naifeng Zhang,A. R. Bayat,Gonzalo Hervás,Ahmed E. Kholif,Marcello Mele,Juan J. Loor,Sokratis Stergiadis,Einar Vargas-Bello-Pérez. 2024

[3]DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants. Ma, Wenlong,Fu, Yang,Bao, Yongzhou,Wang, Zhen,Lei, Bowen,Zheng, Weigang,Wang, Chao,Liu, Yuwen. 2023

[4]Editorial: Insights in functional and applied plant genomics: 2023. Huihui Li. 2025

[5]MtCro: multi-task deep learning framework improves multi-trait genomic prediction of crops. Chao, Dian,Wang, Hao,Wan, Fengqiang,Yan, Shen,Fang, Wei,Yang, Yang. 2025

[6]A comparative study highlights superiority of LSTM in crop genomic prediction. Ruiqing Pan,Yaolong Yang,Yuanyuan Zhang,Qun Xu,Yue Feng,Junyu Chen,Wei Li,Shoupu He,Xinghua Wei,Mengchen Zhang. 2025

[7]Genomic and Pathogenic Diversity of Barley Yellow Mosaic Virus and Barley Mild Mosaic Virus Isolates in Fields of China and Their Compatibility with Resistance Genes of Cultivated Barley. Jiang C., Lei M., Luan H., Pan Y., Zhang L., Zhou S., Cai Y., Xu X., Shen H., Xu R., Feng Z., Zhang J., Yang P.. 2022

[8]Monocot and dicot MLO powdery mildew susceptibility factors are functionally conserved in spite of the evolution of class-specific molecular features. Appiano, Michela,Martinez, Miguel Santillan,Visser, Richard G. F.,Bai, Yuling,Catalano, Domenico,Lotti, Concetta,Zheng, Zheng,Ricciardi, Luigi,Pavan, Stefano. 2015

[9]The use of chloroplast microsatellite markers for assessing cytoplasmic variation in a watermelon germplasm collection. Hu, J-B,Li, J-W,Li, Q.,Hu, J-B,Li, J-W,Li, Q.,Ma, S-W,Wang, J-M.

[10]Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers. Zhang, Chi-Hong,Li, Dao-Yuan,Pan, Da-Jian,Jia, Ji-Zeng,Dong, Yu-Shen.

[11]Identification of candidate MLO powdery mildew susceptibility genes in cultivated Solanaceae and functional characterization of tobacco NtMLO1. Appiano, Michela,Visser, Richard G. F.,Bai, Yuling,Pavan, Stefano,Bracuto, Valentina,Ricciardi, Luigi,Catalano, Domenico,Zheng, Zheng,Lotti, Concetta.

[12]Crop Wild Relatives-Undervalued, Underutilized and under Threat?. Ford-Lloyd, Brian V.,Armstrong, Susan J.,Kell, Shelagh P.,Maxted, Nigel,Schmidt, Markus,Barazani, Oz,Hadas, Rivka,Engels, Jan,Hammer, Karl,Khoshbakht, Korous,Kang, Dingming,Li, Yinghui,Qiu, Lijuan,Long, Chunlin,Lu, Bao-Rong,Ma, Keping,Ge, Song,Wei, Wei,Viet Tung Nguyen,Zhang, Zongwen.

[13]Variation in Adzuki Bean (Vigna angularis) Germplasm Grown in China. Redden, Robert J.,Basford, Kaye E.,Kroonenberg, Pieter M.,Islam, F. M. Amirul,Wang, Shumin,Cao, Yongsheng,Zong, Xuxiao,Wang, Xiaoming.

[14]Functional markers in wheat: current status and future prospects. Liu, Yanan,He, Zhonghu,Xia, Xianchun,He, Zhonghu,Appels, Rudi.

[15]Histological and Ultrastructural Observation Reveals Significant Cellular Differences between Agrobacterium Transformed Embryogenic and Non-embryogenic Calli of Cotton. Shang, Hai-Hong,Liu, Chuan-Liang,Zhang, Chao-Jun,Li, Feng-Lian,Hong, Wei-Dong,Li, Fu-Guang.

[16]Comparisons of cadmium tolerance and accumulation at seedling stage in wheat varieties grown in different decades in China. Jiang, Dong,Ci, Dunwei,Jiang, Dong,Dai, Tingbo,Cao, Weixing,Liu, Fulai,Ci, Dunwei.

[17]QTL mapping for fiber quality traits across multiple generations and environments in upland cotton. Fu-Ding Sun,Jian-Hong Zhang,Shu-Fang Wang,Wan-Kui Gong,Yu-Zhen Shi,Ai-Ying Liu,Jun-Wen Li,Ju-Wu Gong,Hai-Hong Shang,You-Lu Yuan.

[18]Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population. Bagheri, Hedayat,El-Soda, Mohamed,van Oorschot, Inge,Hanhart, Corrie,Keurentjes, Joost J. B.,Koornneef, Maarten,Aarts, Mark G. M.,Bagheri, Hedayat,El-Soda, Mohamed,Bonnema, Guusje,Jansen-van den Bosch, Tanja,Mank, Rolf,Meng, Lin,Wu, Jian,Koornneef, Maarten. 2012

[19]A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. Wei, Dayong,Cui, Yixin,He, Yajun,Ding, Yijuan,Li, Jiana,Qian, Wei,Wei, Dayong,Xiong, Qing,Qian, Lunwen,Tong, Chaobo,Lu, Guangyuan,Jung, Christian.

[20]Genetic and comparative genomics mapping reveals that a powdery mildew resistance gene Ml3D232 originating from wild emmer co-segregates with an NBS-LRR analog in common wheat (Triticum aestivum L.). Guan, Haiying,Li, Jingting,Zhu, Jie,Xie, Chaojie,Yang, Tsomin,Sun, Qixin,Liu, Zhiyong,Zhang, Hongtao,Guan, Haiying,Li, Jingting,Zhu, Jie,Xie, Chaojie,Yang, Tsomin,Sun, Qixin,Liu, Zhiyong,Zhang, Hongtao,Guan, Haiying,Li, Jingting,Zhu, Jie,Xie, Chaojie,Yang, Tsomin,Sun, Qixin,Liu, Zhiyong,Zhang, Hongtao,Guan, Haiying,Li, Jingting,Zhu, Jie,Xie, Chaojie,Yang, Tsomin,Sun, Qixin,Liu, Zhiyong,Zhou, Yilin,Duan, Xiayu.

作者其他论文 更多>>