Deep learning for plant genomics and crop improvement

Our era has witnessed tremendous advances in plant genomics, characterized by an explosion of high-throughput techniques to identify multi-dimensional genome-wide molecular phenotypes at low costs. More importantly, genomics is not merely acquiring molecular phenotypes, but also leveraging powerful data mining tools to predict and explain them. In recent years, deep learning has been found extremely effective in these tasks. This review highlights two prominent questions at the intersection of genomics and deep learning: 1) how can the flow of information from genomic DNA sequences to molecular phenotypes be modeled; 2) how can we identify functional variants in natural populations using deep learning models? Additionally, we discuss the possibility of unleashing the power of deep learning in synthetic biology to create novel genomic elements with desirable functions. Taken together, we propose a central role of deep learning in future plant genomics research and crop genetic improvement.