Leveraging molecular tools for cereal breeding: Progress, limitations, and prospects

Abstract

Rice, wheat, and maize cereals are the major foundation of global food security. However, climate change makes it more challenging to achieve high crop yield, the challenge occurs due to improper management of cereal diseases and pests, and limitations of traditional breeding processes. This study aimed to update the process, limitations, and prospects of molecular tools for cereal breeding, and to explore the significance of marker-assisted selection, marker-assisted backcrossing, gene pyramiding, genomic selection, and modern breeding for improving yield, stress tolerance, and grain quality of cereals. Based on recent studies, we have explored the advances and applications of high-throughput genotyping platforms like the single nucleotide polymorphism (SNP) array and genotyping by sequencing technology in cereals. In this study, we found several limitations, such as a low number of studies with large amounts of data, genotype-environment interactions, lack of study findings at the field level, cost implications, and integration of complex multi-omics data. This study further reveals that many crucial agronomic traits are polygenic in their mode of inheritance, and the hidden genetic links make selection weak and uncertain. However, the application of molecular tools such as CRISPR/Cas genome editing, speed breeding, pan-genomics, artificial intelligence, and high-throughput phenomics provides sustainable solutions to these challenges in cereal improvement. The application of these modern breeding tools, combined with microbiome-assisted breeding and agricultural technologies in precision cereal breeding, opens new opportunities for enhancing yield and climate-smart, sustainable cereal production for global food and nutrition security.