Prospects and challenges of epigenomics in crop improvement

Integrating machine learning and genome editing for crop improvement

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait improvements. Simultaneously, the exponential growth of computational power and big data now promote the application of machine learning for biological research. In this regard, machine learning shows great potential in the refinement of genome editing systems and crop improvement. Here, we review the advances of machine learning to genome editing optimization, with emphasis placed on editing efficiency and specificity enhancement. Additionally, we demonstrate how machine learning bridges genome editing and crop breeding, by accurate key site detection and guide RNA design. Finally, we discuss the current challenges and prospects of these two techniques in crop improvement. By integrating advanced genome editing techniques with machine learning, progress in crop breeding will be further accelerated in the future.

Progress in Rice Breeding Based on Genomic Research

The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.

Genomic perspectives on epigenetics

For much of the twentieth century, it was accepted that genes dictate phenotypes. Nevertheless, genetics in combination with molecular biology and genomics has facilitated the explanation of some peculiar molecular phenomena. Most eukaryotic genomes are crammed with noncoding DNA, which was previously hypothesized to be selfish DNA, with only a small fraction of sequences encoding proteins. We now know that the genes are not blueprint for phenotypes. Typically, genes interact with the environment to form phenotypes. Epigenetic regulation modifies genes. Epigenetics is defined as a "stably heritable phenotype resulting from changes in chromosomes without alterations to DNA sequences". The theme of this special issue is "Genomic perspectives on epigenetics." Here, we review 12 articles that reflect considerable advancements in this rapidly evolving subject area.