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After complete sequencing of its genome and annotation  of the majority of its ~32,000 genes, rice genome has become the model genome  among the cereal genomes, and the focus has shifted from structural to  functional genomics and application of genomic-derived information in rice  breeding. During the past 2 decades, intensive worldwide efforts have led to  significant improvements in rice. An abundance of molecular markers and  information related to many genes/quantitative trait loci that control  agronomically important traits such as yield, quality, and biotic and abiotic  stress tolerance have been identified. Bridging the application gap between  quantitative trait locus identification and marker-assisted selection breeding  is an urgent, arduous, and long-term task. Marker development, allele mining,  gene discovery, and molecular breeding have progressed to a great extent  because of the rapid development of next-generation sequencing, large-scale  high-density genotyping, and genome-wide selection strategies. The availability  of high-density markers and the rapidly decreasing cost of genotyping have  facilitated marker-assisted selection of many traits that were previously not  possible.

Updates and perspectives on the utilization of molecular makers of complex traits in rice