Abstract
Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.
Highlights
Rice (Oryza sativa) is the well-known holder of two important titles: the most important food crop in the world and a model cereal species
We propose that near-isogenic lines (NIL) developed using such approaches are referred to as “precision introgression lines” (PILs)
Since existing estimates of linkage disequilibrium (LD) in rice indicate that LD extends to 100 kb or longer [171, 172], the single nucleotide polymorphism (SNP) dataset should be sufficient for identifying a collection of tag SNPs that define haplotype blocks across the rice genome
Summary
Rice (Oryza sativa) is the well-known holder of two important titles: the most important food crop in the world and a model cereal species. The beginning of the 21st century has been considered the dawn of the genomics era due to the enormous amount of genomics research in bacterial, plant, and animal species, as well as the rapid development of high-throughput equipment for whole-genome genotyping, gene expression, and genome characterization, and the establishment of advanced bioinformatics tools and databases. These rapid developments have irreversibly influenced and redefined plant breeding in the 21st century as “molecular plant breeding” or “genomics-assisted breeding” [14]. We consider the obstacles to the successful application of molecular genetics and genomics research in rice breeding programs and propose ideas on how some of these problems should be solved
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