Since the development of molecular biology, the potential of molecular breeding (MB) contributing significantly to crop improvement has been controversial. With the identification of the first quantitative trait loci (QTL) in the 1980s, the ability of molecular markers to streamline the selection of complex traits has been oversold because scientists have largely underestimated the impact of gene networks and their interactions on plant phenotype. Some of these limitations have now been overcome, thanks to the development of more sophisticated statistical approaches, which allow characterizing both QTL and the QTL by environment interactions (QEI), as well as the contributions made by plant models. Today, the use of markers to track transgenes or stack favorable alleles determining a significant proportion of the phenotypic variance is routine for many crops. The number of reports asserting the successes of MB in dealing with polygenic traits has been definitely increasing. In addition, it is now generally accepted that the role of MB extends beyond the manipulation of elite alleles at a few loci in biparental segregating populations. The modern breeding concept, which includes a combination of phenotypic and molecular selection, needs to evolve new strategies to fully exploit the massive amount of information emerging from the \"-omics\" technologies and various genome sequencing efforts. QTL, functional genomics, and association studies are complementary approaches, which can quantify the genetic effects of specific alleles at target loci. Once the genetic gain of favorable alleles has been validated in a suitable biological context and environment, allele-based markers can be easily developed and employed. This validation step remains a major bottleneck in the establishment of a large set of markers appropriate for deployment in plant breeding. However, considering the technological and methodological progress achieved in genomics in recent years, it is clear that the potential of MB to complement phenotypic selection and improve crop productivity is set to increase significantly in the near future.
Booklet produced for the Annual Barwale Foundation Lecture Day, Barwale Foundation, New Delhi, India, March 21st 2007. 24 pp.