Application of Next-Generation Sequencing Technology for Rice Improvement

Rice is one of the most significant food crops worldwide. Population growth and climate change posed great challenges for further rice production. In the past decade, we have observed enormous developments in next-generation sequencing technologies (NGS) and genomics, revolutionizing almost every aspect of crop improvement. The launching of new platforms employing long-read sequencing safeguarded further efficient sequencing of huge and complex genomes. Currently, rice genetic resources and germplasms are first characterized by sequencing platforms, pursued by bioinformatics tools and genomic methodology. These are applied to acquire masses of genomic data from these various resources. These data are further explored for insights into the molecular mechanisms of quantitative and qualitative traits of rice. The deep integration of genomic technologies and NGS into rice study and breeding practices has changed the scheme and framework of rice breeding. Additionally, these genomic data offer molecular knowledge and wide range of applications like rice marker discovery by NGS, wide crosses and alien introgression, transcriptome investigation, gene expression profiling, small non-coding RNA profiling, gene annotation using transcriptome sequence data, phylogenetic and ecological studies, allele mining, epigenetics studies, metagenomics analysis, single-cell genomics, exome sequencing, and whole genome resequencing (WGRS). NGS permits the straight identification of candidate genes through strategies such as MutMap, Genome-Wide Association Studies (GWAS), and QTL-sequencing. Understanding the molecular mechanisms behind rice character expression will boost rice breeding for developing climate resilient crops and enhancing yield compared to old conventional breeding methods.