Current Status and Future Directions of Molecular Breeding Tools in Rice

Tremendous advances have been made in molecular genetics and genomics across the rice research community, yet few breeding groups have fully integrated molecular breeding tools into their programs.  This talk will review the current status of molecular breeding tools and explore future directions that promise the greatest impact in accelerating progress in plant breeding.  Rice is a good example of how basic research has led to practical applications in crop improvement—such as the wealth of cloned genes and QTLs for agronomic traits.  The availability of whole genome marker scans using SNP chips and sequencing has also enabled genome-wide association mapping across diverse germplasm panels, leading to valuable information on SNP haplotypes predictive of beneficial alleles for crop improvement.  Coupled with low-cost SNP genotyping platforms, these resources can enable more efficient targeted selection at major genes along with genome-wide selection approaches for more complex traits.  Even with recent advances, however, major initiatives are still needed to fully realize the potential of molecular breeding tools in mainstream breeding programs.  Further efforts are needed in several key areas, including (1) developing resources to share trait-predictive SNP haplotypes and marker validation information for each crop; (2) leveraging advances in high-throughput phenotyping, sequencing, and population development to implement large-scale allele mining of crop genebanks; (3) improving public-sector breeding informatics tools and databases to incorporate high-density SNP data, imputation, and tracking of targeted SNP haplotypes; and (4) exploring the use of genome editing for rapid pyramiding of beneficial alleles at breeding-relevant genetic loci.