What if we knew all the genes for a quantitative trait in hybrid crops?

Plant genomics programs are expected to decipher the sequence and function of genes controlling important traits. Most of the important traits in crops are quantitative and are controlled jointly by many loci. What if we knew all the genes for a quantitative trait in hybrid crops? Will genomics enhance hybrid crop breeding, which currently involves selection on the basis of phenotypes rather than gene information? With maize (Zea mays L.) as a model species, I found through computer simulation that gene information is most useful in selection when few loci (e.g., 10) control the trait. With many loci (≥50), the least squares estimates of gene effects become imprecise. Gene information consequently improves selection efficiency among hybrids by only 10% or less, and actually becomes detrimental to selection as more loci become known. Increasing the population size and trait heritability to improve the estimates of gene effects also improves phenotypic selection, leaving little room for improvement of selection efficiency via gene information. The typical reductionist approach in genomics therefore has limited potential for enhancing selection for quantitative traits in hybrid crops.