SNP Haplotype Validation for Rice Improvement.

Tremendous advances have been made in genetics and genomics research across the rice community, yet few breeding groups have fully integrated molecular breeding tools into their programs.  The availability of high resolution single nucleotide polymorphism (SNP) data has enabled genome-wide association studies (GWAS) across diverse germplasm panels, leading to valuable information on SNP haplotypes that are predictive for key traits.  When combined with whole genome sequence data from the 3,000 Rice Genomes Project and recent advances in genome editing, we now have an excellent opportunity to identify and validate beneficial SNP haplotypes at major genes and QTLs for rice improvement.  However, a community-wide effort is needed to characterize SNP-tagged alleles at significant QTL and GWAS loci and validate them in elite breeding lines and segregating populations in target environments. A new initiative to share information on breeding-relevant SNP haplotypes for the rice community, called the RiceSNPvisor, is proposed to compile data on beneficial SNP haplotypes, help guide SNP validation efforts, and ultimately provide breeders with an online tool for selecting validated SNP markers that match their target traits, germplasm, and environments. The objective is to enable rice breeders to more readily employ high-throughput SNP genotype data to track targeted alleles at key genes for deployment in their mainstream breeding pipelines.  Moreover, recent advances in genome editing promise to accelerate the process to validate breeding-relevant genes and SNP haplotypes and ultimately lead to novel approaches to rapidly combine beneficial alleles from diverse germplasm into high-yielding genetic backgrounds without the negative linkage drag that comes from marker-assisted backcrossing.