This new edition focuses on applied bioinformatics with specific applications to crops, model and diverse plant species. The scope extends from the genome to the phenome and includes aspects of data management, analysis, visualization, and integration. The methods and approaches found within reflect the increasing use of high performance computing infrastructure to analyze and manage the enormous volume of data being generated by the latest high throughput technologies, the establishment and further maturation of major database systems and repositories, as well as the introduction of new approaches such as machine learning. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detailed implementation advice that leads to successful research results. Authoritative and up-to-date, Plant Bioinformatics: Methods and Protocols, Third Edition will aid researchers exploring the broad comparison of species that will drive future plant research, crop breeding, and bioinformatics developments that allow us to understand and manipulate the heritable differences between individuals and populations. Chapters 2, 3, and 26 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.