Bioinformatics for Plant Research and Crop Breeding

Abstract

Bioinformatics plays a crucial role in crop improvement and breeding by facilitating the analysis and interpretation of vast genetic data. It accelerates these processes by aiding in selecting desirable traits, such as yield, tolerance to abiotic and biotic stresses, and improved nutritional content. Bioinformatics tools empower researchers to delve into the genetic makeup of plants, encompassing genetic engineering, gene expression, genetic variation, and intricate interactions between genes and their environment. Additionally, it assists in devising effective plant disease diagnostic strategies and may contribute to future breeding decision management systems by predicting and monitoring plant health and quality. Bioinformatics tools are instrumental in single nucleotide polymorphism (SNP) mining and subsequent utilization in high-throughput SNP genotyping for varietal identification, differentiation, and evolutionary studies. The manifold applications of bioinformatics in crop improvement encompass genetic diversity analysis, phylogenetic relationship estimation through the use of bioinformatics software, as well as the prediction of heterosis and heterotic combinations within breeding programs. Genomics constitutes a pivotal realm of bioinformatics in crop improvement, encompassing the comprehensive examination of entire genomes. Genomic analysis unveils vital information about the location and function of genes, allowing breeders to pinpoint desirable genetic traits and formulate strategies for breeding innovative varieties that enhance crop performance. Furthermore, bioinformatics expedites crop breeding by forecasting desired traits through molecular markers and marker-assisted selection (MAS). Other indispensable areas of bioinformatics that contribute to crop improvement and breeding encompass transcriptomics, proteomics, and metabolomics. Transcriptomics explores gene expression, while proteomics and metabolomics delve into studying proteins and metabolites. These facets of bioinformatics offer insights into the biochemical processes occurring within plants. Moreover, genomic tools like MAS, GWAS, and genomic selection are used to identify genes and proteins that are linked to desirable traits. It is facilitating the development of new crop varieties. Bioinformatics enables genome editing via technologies such as CRISPR-Cas9. It assists in designing efficient gRNA and genome editing constructs, predicting on-target and off-target outcomes, and potentially enhancing crop improvement. In summary, through the analysis of genetic data and the utilization of diverse tools, bioinformatics aids researchers in identifying desirable traits, creating new crop varieties, and expediting crop breeding efficiency. Despite its tremendous impact on crop improvement and breeding, the interpretation and management of large amounts of genetic data continue to pose difficulties, demanding the development of improved approaches and novel bioinformatics tools for long-term agricultural progress. © 2024 John Wiley & Sons Ltd.