Genome to phenome: bioinformatics of crop plants

Abstract

Due to the expanding world population, agricultural output must increase to fulfill the growing need for food. Crop breeding is a sustainable way to boost production and yield stability without increasing the usage of fertilizers and pesticides. Recent developments in genetics and bioinformatics provide prospects for expediting crop improvement. Because of this, there are more and more high-quality crop reference genomes accessible, which is advantageous for downstream analysis like variant calling and association mapping that reveal potential breeding targets in the genome. Recent years have witnessed a paradigm change toward using omics information, computational tool, and technology to increase agricultural production and yield. Although this upward trend, computational tool and pipelines for genome assembly, gene annotation, and downstream analysis continue to struggle with plant genomes. In this chapter, we provide a bird’s-eye view of the services and infrastructure required to build and analyze plant genomes and demonstrate correlation between genotypes and phenotypes. All of these developments will enable breeders to quickly generate more robust, enhanced crops that can withstand the demands of a rising population and a challenge environment. © 2023 Elsevier Inc. All rights reserved.