With the dawn of the 21st century, agricultural research has accelerated due to emerging biotechnological tools. Notably, molecular markers have significantly advanced crop improvement programs, achieving food and nutritional security at an accelerated pace. Progress in the application of molecular markers in agriculture transitioned from simple sequence repeat markers to single nucleotide polymorphism markers with the arrival of next-generation sequencing technologies. This development initiated a second phase of acceleration for crop improvement programs, supporting the development of cultivars with enhanced productivity, stress resilience, and improved food and nutritional quality. Advances in biotechnological tools have enabled the development of new, diversified crops. The power of genomics, at an affordable cost, has garnered considerable attention as a focal point for present-day crop improvement programs.

Genomics-assisted crop improvement programs have become the hub for accelerated scientific progress, delivering improved cultivars incorporating desirable traits in a minimal time frame. There have been parallel developments in both newer genomics tools and their application in crop improvement. Recognizing the need to have a Research Topic that aims to pool the research progress on genomics tool development and its application to crop improvement, we envision this Research Topic acting as a connecting link, especially as we move forward from next-generation sequencing platforms to third-generation sequencing platforms. Understanding the potential impact of these advances, this Research Topic is proposed to deliver examples of the practical utilization of these emerging genomics tools in crop improvement programs. The availability of newer genomic tools will foster the creation of novel ways to use them in crop improvement. Research reports on genomics-assisted applications in crop improvement and newer biotechnological or computational tools are anticipated for publication in this research topic.

This Research Topic aims to explore the development and application of genomics tools in crop improvement programs. Specifically, it seeks to highlight the practical utilization of emerging genomics tools, such as next-generation and third-generation sequencing platforms, in enhancing crop productivity, stress resilience, and nutritional quality. The goal is to gather research that demonstrates the power of genomics to drive crop improvement at an accelerated pace, through allele mining, marker-trait association, and the use of newer genomic or computational tools that facilitate breeding for new crops or cultivars.

To gather further insights into the boundaries of genomics applications in crop improvement, we welcome articles addressing, but not limited to, the following themes:

• Chromosome-scale genome (re)sequencing and its application in allele mining to identify candidate genes, alleles, or germplasm for the improvement of various traits associated with climate resilience, abiotic and biotic stress tolerance, weed management, enhanced photosynthesis, biomass production, nutritional and functional quality traits, or de novo domestication.

• Identification of genome-wide markers and their association with desirable traits for use in crop improvement programs.

• Transcriptome-based methods such as RNA-seq for gene or allele discovery and model-based genomic selection approaches with special applications in agriculture.

• Development of new genomics or computational tools for applications in agriculture.

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Frontiers in Plant Science

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