Opportunities for Whole Genome Sequence-Assisted Breeding in Maize.

In recent years, the development of technologies such as seed chipping, high-throughput genotyping and robust IT systems has enabled marker-assisted breeding to be implemented on a meaningful scale in breeding programs for crops such as maize. Using moderately-dense marker sets, it has been demonstrated that genetic gain in maize can be increased. Completion of the maize genome sequence generated a new wave of SNP discovery, opening the door to enhanced genomic selection for breeding value estimation. As next-generation DNA sequencing technologies become practical for high-throughput use, it should be feasible to obtain sequence information on hundreds of plants at a time. This creates opportunities for both crop breeding programs and biotechnology research. More robust whole-genome association studies, detailed exploration of germplasm diversity and recombination at the genome-level, and precise introgression of key genes into germplasm are potential applications. Additionally, novel gene and allele discovery can facilitate functional genomics studies and provide new candidate gene targets for biotechnology traits. Prospects for these technologies are great, but it should not distract from obtaining high quality phenotypes, management of germplasm resources, and the transformation of data into knowledge.