Computational tools for plant genomics and breeding

Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along thecentral dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advancesfurther revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic predictionand selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraintsof biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rationaldesign of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for anew era of crop breeding where agronomic traits are enhanced by genome design.