Rice Genetics IV - IRRI books - International Rice Research Institute

volume). Those SSRs that can be scored using agarose gels will be particularly usefulin marker-assisted breeding (Gupta et al 1999).False-positives in MAS. If the distance between the linked marker and the targetgene is not small enough, a crossover will result in false-positives during MAS. Anotherreason for the false-positive screening is incorrect results of gene mapping. Finemapping or high-resolution mapping of the gene and the discovery of the more closelylinked markers using larger populations will reduce the occurrence of false-positives.Furthermore, phenotypic evaluation should be performed with more reliable methods,with multiple replications, and under different environments in order to locategenes more precisely. New efficient gene/QTL mapping strategies and quantitativegenetic analysis methods should also be proposed and adopted.Expense of MAS. The relatively high expense is another factor limiting the developmentand application of MAS. The expense includes not only the materials andsupplies but also less definable costs such as quality of technical support, lab space,and radioisotope permits (Mohan et al 1997a). However, advances in technologieswill result in a decrease in the costs of MAS. PCR-based markers such as microsatellitesand AFLP are amenable to automation. In addition, DNA extraction methods havebeen improved. Not only have rapid DNA extraction methods for rice been developed(Williams and Ronald 1994, Zheng et al 1995, Lange et al 1998), but it is also possibleto isolate DNA directly from the seeds before sowing (Chunwongse et al 1993).With these developments, DNA marker technology without electrophoresis shouldcome into use in the future.Restriction of number of genes in the screening program. The number of genes(loci) involved in the MAS program is another factor that should be considered. Forexample, with only four or five loci being selected, the population sizes and numberof F 1 seeds needed for a MAS program will be considerable and any further additionwill lead to an exponential increase (Mackill et al 1999). This indicates that only themost important traits or loci should be identified and selected in a MAS program.More importantly, marker-assisted selection should be considered as a complement toconventional breeding rather than a replacement for it.ConclusionsMolecular marker technology has changed the way plant genetics research is conducted.Genetics studies in rice should include placing newly identified genes on themolecular map. The technology is already leading to the cloning of important genes.However, the application of these tools in conventional breeding programs has beenlimited. The challenge for the future is to integrate these tools into ongoing rice improvementprograms to accelerate the development of cultivars possessing uniquecombinations of genes in a productive and adapted genetic background.Aside from its direct application to rice breeding programs, molecular mapping ofmajor genes will ultimately allow the identification of the DNA sequence and resultingprotein product responsible for the observed phenotype. Map-based cloning ofgenes has been a laborious undertaking, but, with the availability of the completeMolecular mapping and marker-assisted selection . . . 145