DNA Sequencing to Tap New Alleles of Known Genes From Diverse Germplasm for Maize Improvement.

Modern plant breeding incorporates the use of many molecular tools to improve crop performance.  Critical to these efforts is the identification and manipulation of genes encoding traits of importance.  However, because the genetic variation in the breeding pool available to most plant breeders is much smaller than that available in the species as a whole, the best allelic variation for optimal expression (including optimal timing and tissue distribution) of important genes may not have been identified and used to date.  Even in the highly variable gene pool of maize (Zea mays), rare alleles of most known loci have been lost in the domestication and plant improvement process.  Returning these alleles to the breeding pool of maize in a haphazard manner has had limited success.  Many of these alleles are rare because they were not useful to the improved performance of the plant under the selection conditions applied; without a method to specifically tag these alleles, they are likely to be lost again in the bottleneck created by modern selection methods.  A more targeted approach to mining the alleles of useful genes is needed.  Now that the maize reference sequence is available, resequencing of genes, genomic regions, and genomes of exotic germplasm will allow the search for new sequence variation in genes of interest.  This identification must be followed by confirmation that the new allele results in a difference in plant phenotype that is beneficial.  Presented here are examples of successful identification of genes and alleles from diverse sources conferring improved phenotypes in maize for provitiamin A content, drought resistance, and aflatoxin accumulation resistance. These three traits are presented to highlight the feasibility and also the difficulties in the approach.